RSS

Classification by Biochemical Functions


Glycolysis

  • Alcohol dehydrogenase class IV sigma chain [Homo sapiens (human)]: PDB:1D1S
  • Triosephosphate isomerase [Gallus gallus (chicken)]: PDB:1TPH
  • Pyruvate dehydrogenase complex [Geobacillus stearothermophilus (bacteria,thermophile)]: PDB:1W85

Citric acid cycle

  • ATP synthase (F0 portion) [Escherichia coli (bacteria)]: PDB:1C17
  • ATP synthase (F1 portion) [Bos taurus]: PDB:1E79
  • Flavoenzyme Ero1p [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1RP4

Electron transport

  • Aldehyde ferredoxin oxidoreductase (AOR) [Pyrococcus furiosus (thermophile, archaea)]: PDB:1AOR
  • ATP synthase (F0 portion) [Escherichia coli (bacteria)]: PDB:1C17
  • ATP synthase (F1 portion) [Bos taurus]: PDB:1E79
  • Cytochrome C oxidase (before oxidized, with carbon monoxide) [Bos taurus]: PDB:1OCO
  • Flavoenzyme Ero1p [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1RP4
  • Cytochrome C oxidase (after oxidized, with peroxide ion) [Bos taurus]: PDB:2OCC

Photosynthesis

  • ATP synthase (F0 portion) [Escherichia coli (bacteria)]: PDB:1C17
  • ATP synthase (F1 portion) [Bos taurus]: PDB:1E79
  • Photosystem II [Synechococcus elongatus (cyanobacteria)]: PDB:1FE1
  • Photosystem I P700 chlorophyll a apoprotein A1 [Synechococcus elongatus (cyanobacteria)]: PDB:1JB0
  • Light harvesting protein B-800/850 [Rhodopseudomonas acidophila (phototrophic bacteria)]: PDB:1KZU
  • Photosynthetic Reaction Center [Rhodopseudomonas viridis (phototrophic bacteria)]: PDB:1PRC
  • light-harvesting complex of photosystem II (LHC-II) [Spinacia oleracea (Spinach) ]: PDB:1RWT
  • Cyanobacterial photosystem II [Thermosynechococcus elongatus (cyanobacteria)]: PDB:1S5L
  • Cytochrome b6f complex [Mastigocladus laminosus (cyanobacteria)]: PDB:1VF5

Biosynthesis of carbohydrate and gluconeogenesis

Metabolism of other carbohydrate

  • Cellulase CelC [Clostridium thermocellum (bacteria, thermophile)]: PDB:1CEO
  • Alpha-amylase [Homo sapiens (human)]: PDB:1SMD
  • Nuclear receptor mSF-1 LBD complexed with PG(ligand) [mouse]: PDB:1YMT
  • Peptideglycan L,D-transpeptidase [Enterococcus faecium]: PDB:1ZAT
  • Ca2+/calmodulin-dependent protein kinase-II (CaMKII) [Caenorhabditis elegans (nematode)]: PDB:2BDW

Lipid biosynthesis and metabolism

  • Lipase [Homo sapiens (human)]: PDB:1HLG
  • Phospholipase A2 [Homo sapiens (human)]: PDB:1POD
  • Lanosterol synthase [Homo sapiens (human)]: PDB:1W6J
  • Acetyl-coenzyme A carboxylase [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1W93
  • 3-ketoacyl-coA thiolase 2 [Arabidopsis thaliana (mouse-ear cress)]: PDB:2C7Y
  • Cholesterol ester transfer protein [Human]: PDB:2OBD
  • β2 adrenergic receptor [Human]: PDB:2RH1

Phosphorylation

  • Protein kinase CheY/CheA complex (bacteria chemotaxis) [Escherichia coli (bacteria)]: PDB:1A0O
  • DBL homology domain from beta-PIX [Homo sapiens (human)]: PDB:1BY1
  • Mitogen-activated protein (MAP) kinase ERK2 [Rattus norvegicus (rat)]: PDB:1ERK
  • Cyclin A/cyclin-dependent kinase 2(CDK-2) complex [Homo sapiens (human)]: PDB:1FIN
  • Cdc42 / Cdc42GAP complex [Homo sapiens (human)]: PDB:1GRN
  • Peutz-Jeghers cancer syndrome (PJS) related protein Mo25 Alpha in Complex with the C-Terminus of the Pseudo Kinase STE-20 Related Adaptor [Homo sapiens (human)]: PDB:1UPK
  • SR (serine/arginine rich) protein kinase SRPK1 / peptide complex [Homo sapiens (human)]: PDB:1WBP
  • SWIRM domain of chromosomal DNA binding protein ADA2α [Human]: PDB:2AQE
  • Ca2+/calmodulin-dependent protein kinase-II (CaMKII) [Caenorhabditis elegans (nematode)]: PDB:2BDW
  • Epac, Guanine-nucleotide-exchange factor for GTP-binding protein Rap [Mus musculus (house mouse)]: PDB:2BYV
  • Lipoate protein ligase A (LplA) [Thermoplasma acidophilum (archaea,thermophile)]: PDB:2C8M
  • Protein phosphatase 2A (heterotrimeric holoenzyme) [Homo sapiens (human) ]: PDB:2IAE
  • Protein Phosphatase 2A [Homo sapiens (human)]: PDB:2NPP
  • Protein Phosphatase 2A with C-terminus truncated catalytic subunit [Homo sapiens (human)]: PDB:2NYM
  • TGF-β3 - TGF-β receptor complex [Human]: PDB:2PJY
  • Protein kinase A [Mouse]: PDB:2QCS
  • Tyrosine-protein kinase c-Src/AMP-PNP complex [Homo sapiens (human)]: PDB:2SRC

Biosynthesis and metabolism of amino acid, nucleic acid, and related molecules

  • D-amino acid aminotransferase [Thermophilic bacterium PS3]: PDB:1DAA
  • Ribonuclease A / ribonuclease inhibitor (RI) complex [Bos taurus]: PDB:1DFJ
  • Catalytic antibody 1F7 (chorismate mutase activity) [Mus musculus (house mouse)]: PDB:1FIG
  • Arginases I and nor-NOHA complex [Rattus norvegicus (rat)]: PDB:1HQH
  • 3-isopropylmalate dehydrogenase [Thermus thermophilus (bacteria,thermophile)]: PDB:1IPD
  • Ribonucleotide reductase [Escherichia coli (bacteria)]: PDB:1MXR
  • Amidohydrolase Tm0936 [Thermotoga maritima]: PDB:1P1M
  • Acetolactate synthase [Arabidopsis thaliana (thale cress, or mouse-ear cress)]: PDB:1YBH
  • mRNA decapping enzyme Dcp2p [Schizosaccharomyces pombe]: PDB:2A6T
  • Epac, Guanine-nucleotide-exchange factor for GTP-binding protein Rap [Mus musculus (house mouse)]: PDB:2BYV
  • Cbf5-Nop10-Gar1 complex (part of the pseudouridylation enzyme) [Pyrococcus furiosus (thermophile, archaea)]: PDB:2EY4
  • B subunit of UvrABC (DNA repair system) complexed with a DNA strand [Bacillus caldotenax (bacteria)]: PDB:2FDC
  • Nicotinamide phosphoribosyltransferase (NMPRTase) [Human]: PDB:2GVG
  • Nicotinamide phosphoribosyltransferase (NMPRTase): Complex with FK866 [Human]: PDB:2GVJ
  • Glutamate decarboxylase 1(GAD) / cofactor PLP complexed [human]: PDB:2OKJ
  • Nitrogenase molybdenum iron protein [Azotobacter vinelandii (aerobic nitrogen-fixing bacteria)]: PDB:3MIN

Control of hormones

  • Androgen receptor [Homo sapiens (human)]: PDB:1E3G
  • Interleukin-1 beta [Homo sapiens (human)]: PDB:1I1B
  • Interleukin-1beta converting enzyme(ICE)/inhibitor peptide complex [Homo sapiens (human)]: PDB:1IBC
  • Interleukin-18 [Homo sapiens (human)]: PDB:1J0S
  • Acetylcholine Receptor [Torpedo californica]: PDB:1OED
  • Molting hormone receptor (EcR/USP) / steroidal ligand ponA complex [Heliothis virescens (noctuid moth)]: PDB:1R1K
  • Lanosterol synthase [Homo sapiens (human)]: PDB:1W6J
  • Nuclear receptor mSF-1 LBD complexed with PG(ligand) [mouse]: PDB:1YMT
  • Human Placental Lactogen [Homo sapiens (human)]: PDB:1Z7C
  • insulin-degrading enzyme in complex with insulin B chain [Homo sapiens (human)]: PDB:2G54
  • Ancestral corticoid receptor / aldosterone complex [unidentified]: PDB:2Q1H
  • Growth hormon complexed with its receptor [Homo sapiens (human)]: PDB:3HHR
  • Insulin [Sus scrofa (pig)]: PDB:4INS

Gene and chromosome

  • deoxyribonucleic acid (DNA) [N/A (synthetic)]: PDB:1BNA
  • Human Telomeric DNA (monomer with 22 bases) [Homo sapiens (human)]: PDB:1KF1
  • Ribonucleotide reductase [Escherichia coli (bacteria)]: PDB:1MXR
  • SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54 [Danio rerio (zebra fish)]: PDB:1Z3I
  • Nucleosome (nucleosome core / DNA complex) [Xenopus laevis (African clawed frog)]: PDB:1ZBB
  • BPTF PHD finger-linker-bromodomain bound to H3K4me3 [Homo sapiens (human)]: PDB:2F6J
  • Histon modification protein WRD5 / histon subunit H3 complex [Human]: PDB:2H13
  • CIA-histone H3-H4 complex [Homo sapiens (human)]: PDB:2IO5
  • Ftsk(C-domain) hexmer [Bacteria(Pseudomonas-aeruginosa)]: PDB:2IUU

DNA metabolism

  • Restriction endonuclease BamHI/DNA complex [Bacillus amyloliquefaciens (bacteria)]: PDB:1BHM
  • deoxyribonucleic acid (DNA) [N/A (synthetic)]: PDB:1BNA
  • Intein PI-SceI homing endonuclease [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1DFA
  • human 8-oxoguanine glycosylase (hOGG1) bound to DNA [Homo sapiens (human)]: PDB:1EBM
  • Replication terminator protein(Tus)/DNA complex [Escherichia coli]: PDB:1ECR
  • DNA repair enzyme [Homo sapiens (human)]: PDB:1EWN
  • Gamma delta resolvase / DNA complex [Escherichia coli]: PDB:1GDT
  • Human Telomeric DNA (monomer with 22 bases) [Homo sapiens (human)]: PDB:1KF1
  • Intein PI-SceI homing endonuclease / DNA complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1LWS
  • Bifunctional DNA primase-polymerase [Sulfolobus islandicus (archaea)]: PDB:1RNI
  • MutY adenine DNA glycosylase/DNA lesion in A*oxoG pair complex [Bacillus stearothermophilus (bacteria)]: PDB:1RRQ
  • Restriction enzyme EcoRV/DNA complex (before DNA cleave, without Mg2+ ion) [Escherichia coli (bacteria)]: PDB:1RVA
  • Restriction enzyme EcoRV / DNA Complex (after DNA cleaved, with Mg2+ ion) [Escherichia coli (bacteria)]: PDB:1RVC
  • SV40 large tumor antigen [Simian virus 40 (virus)]: PDB:1SVM
  • clamp loader (RFC) bound to the DNA sliding clamp (PCNA) [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1SXJ
  • TAQ polymerase (DNA synthesizer)/DNA complex [Thermus aquaticus (bacteria)]: PDB:1TAU
  • Deoxyribodipyrimidine photolyase/DNA complex [Synechococcus sp. PCC 6301 (cyanobacteria)]: PDB:1TEZ
  • DNA repairing complex RecBCD [Escherichia coli (bacteria)]: PDB:1W36
  • SUMO1-conjugated thymine DNA glycosylase [Homo sapiens (human)]: PDB:1WYW
  • Type I restriction-modification enzyme, specificity subunit [Methanococcus jannaschii (archaea)]: PDB:1YF2
  • SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54 [Danio rerio (zebra fish)]: PDB:1Z3I
  • Telomere repeat-binding protein [Arabidopsis thaliana (thale cress)]: PDB:2AJE
  • Pentapeptide repeat protein for resistance against quinolones, MfpA [Mycobacterium tuberculosis (bacteria)]: PDB:2BM4
  • Transcription-repair coupling factor [Escherichia coli]: PDB:2EYQ
  • Restriction enzyme Ecl18kI-DNA complex [Enterobacter cloaceae]: PDB:2FQZ
  • Papillomavirus E1 hexameric helicase [Bovine papillomavirus type I]: PDB:2GXA
  • E. coli DNA polymerase III, beta-subunit [Escherichia coli (bacteria)]: PDB:2POL
  • Reverse transcriptase [Human Immunodeficiency Virus type 1]: PDB:3HVT

RNA metabolism

  • Sex-lethal (Sxl) protein/RNA complex [Drosophila melanogaster (fruit fly)]: PDB:1B7F
  • Catabolite gene activator protein complex with DNA [Escherichia coli (bacteria)]: PDB:1CGP
  • Ribosome recycling factor (RRF) [Thermotoga maritima (thermophile, bacteria)]: PDB:1DD5
  • Mammalian Poly(A) Polymerase [Bos taurus (bovine)]: PDB:1F5A
  • Transcription factor c-Fos-c-Jun / DNA complex [Homo sapiens (Human)]: PDB:1FOS
  • DNA-DIRECTED RNA POLYMERASE II [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1I6H
  • Hypothetical RNA 2'-O-ribose methyltransferase (RrmA) [Thermus thermophilus (bacteria)]: PDB:1IPA
  • 5-methyluridine methyltransferase TrmA [Escherichia coli]: PDB:3BT7
  • RNA hammerhead ribozyme [Mus musculus (house mouse)]: PDB:1MME
  • mRNA decapping enzyme Dcp1p [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1Q67
  • Transcription factor IIB / RNA polymerase II complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1R5U
  • RNA polymerase II-transcribing complex in the post-translocation state [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1SFO
  • Argonaute (RNA interference protein) [Pyrococcus furiosus DSM 3638 (archaea, thermophile)]: PDB:1U04
  • Group I self-splicing intron in complex with its exons [Homo sapiens (Human)]: PDB:1U6B
  • CCA-adding enzyme [Archaeoglobus fulgidus (Archaea)]: PDB:1UET
  • Fungal galectin CGL2 [Coprinopsis cinerea (Inky cap fungus)]: PDB:1UL9
  • Tryptophanyl-tRNA synthetase (mini TrpRS) [Homo sapiens (human)]: PDB:1ULH
  • Phage twort group I ribozyme (self-splicing intron) complexed with it's product [Bacteriophage Twort (virus)]: PDB:1Y0Q
  • Transcriptional activator GCN4/DNA complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1YSA
  • Human Argonaute2 to form minimal RISC [Pyrococcus furiosus (archaea)]: PDB:1Z25
  • The zinc finger (DNA binding site) of transcription factor Zif268/DNA complex [Mus musculus (house mouse)]: PDB:1ZAA
  • Archaeal Rrp4 Exosomes [Archaeoglobus fulgidus (archaea)]: PDB:2BA0
  • A Piwi domain (part of RNAi protein argonaut)/siRNA-like duplex complex [Archaeoglobus fulgidus]: PDB:2BGG
  • RNase III (D44N) complexed with double-stranded RNA [Aquifex aeolicus (bacteria,thermophile)]: PDB:2EZ6
  • Dicer [Giardia intestinalis (flagellate)]: PDB:2FFL
  • RNase Z / tRNA(Thr) complex [Bacillus subtilis]: PDB:2FK6
  • Transcription regulating factor CSL-Notch-Mastermind/DNA complex [Caenorhabditis elegans (nematode)]: PDB:2FO1
  • Mitochondrial RNA binding protein (MRP1/MRP2) - guideRNA complex [Trypanosoma brucei (Africa sleeping sickness parasitic protozoa)]: PDB:2GJE
  • RNA ligase Rnl2 complexed with AMP [Bacteriophage T4 (virus)]: PDB:2HVQ
  • H/ACA box RNP [Pyrococcus furiosus (archaea,thermophile)]: PDB:2HVY
  • Retinoic acid receptor-gamma / retinoic acid complex [Homo sapiens (human)]: PDB:2LBD

Protein metabolism

  • Hepatitis C virus NS3 protease [Hepatitis C virus(HCV)]: PDB:1A1R
  • Chaperonin (GroEL-GroES) / ADP complex [Escherichia coli (bacteria)]: PDB:1AON
  • Ubiquitin ligase(E6AP)/ubiquitin-conjugating enzyme(UbcH7) complex [Homo sapiens (human)]: PDB:1C4Z
  • Ribosome recycling factor (RRF) [Thermotoga maritima (thermophile, bacteria)]: PDB:1DD5
  • Eukaryotic protein Release Factor eRF1 [Homo sapiens (human)]: PDB:1DT9
  • Thiol:disulfide interchange protein DsbC [Escherichia coli (bacteria)]: PDB:1EEJ
  • tRNA (phenylalanine) [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1EHZ
  • Complex of (Arginyl-tRNA synthetase/tRNA/Arginine) [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1F7U
  • Heat shock protein HSP33 [Escherichia coli (bacteria)]: PDB:1HW7
  • Ubiquitin ligase complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1LDD
  • 20S proteasome [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1RYP
  • Trypsin [Homo sapiens (human)]: PDB:1TRN
  • SARS coronavirus main proteinase [Severe acute respiratory syndrome coronavirus(SARS-CoV)]: PDB:1UJ1
  • Tryptophanyl-tRNA synthetase (mini TrpRS) [Homo sapiens (human)]: PDB:1ULH
  • Ribosomal chaperon trigger factor complexed with 50S ribosome [Escherichia coli (bacteria)]: PDB:1W26
  • Simian virus 5 V protien complexed with human DDB1 [Simian virus 5 / Homo sapiens (human)]: PDB:2B5L
  • CmcI, cephamycin biosynthesis-related enzyme [Streptomyces clavuligerus]: PDB:2BR4
  • Lipase (LipA) / lipase chaperon (Lif) complex [Burkholderia glumae (bacteria)]: PDB:2ES4
  • beta-secretase 2 (BACE2) [Homo sapiens (human)]: PDB:2EWY
  • insulin-degrading enzyme in complex with insulin B chain [Homo sapiens (human)]: PDB:2G54
  • Thiamine pyrophosphate-specific riboswitch [Escherichia coli (bacteria)]: PDB:2GDI
  • NS2-3 protease [Hepatitis C virus(HCV)]: PDB:2HD0
  • Trapped UBL activation complex [Human]: PDB:2NVU
  • Gamma-B crystallin (eye lens components protein) [Bos taurus (Bovine)]: PDB:4GCR
  • Alpha-thrombin/hirudin complex [Homo sapiens (human)/Hirudo medicinalis (leech)]: PDB:4HTC
  • HIV-1 PROTEASE [Human Immunodeficiency Virus type 1]: PDB:7HVP
  • Papain [Carica papaya (Papaya)]: PDB:9PAP

Control of gene expression

  • Trp RNA-Binding Attenuation Protein/RNA complex [Bacillus stearothermophilus (bacteria)]: PDB:1C9S
  • Catabolite gene activator protein complex with DNA [Escherichia coli (bacteria)]: PDB:1CGP
  • Met repressor-operator complex [Escherichia coli (bacteria)]: PDB:1CMA
  • Ribonuclease A / ribonuclease inhibitor (RI) complex [Bos taurus]: PDB:1DFJ
  • Androgen receptor [Homo sapiens (human)]: PDB:1E3G
  • Bleomycin hydrolase Gal6 [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1GCB
  • Oct4/Sox2/DNA complex [Mouse, Human]: PDB:1GT0
  • lac repressor [Escherichia coli (bacteria)]: PDB:1LBI
  • YibK methyltransferase (knot protein) complexed with an inhibitor (AdoHcy) [Haemophilus influenzae (bacteria)]: PDB:1MXI
  • Transcription factor IIB / RNA polymerase II complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1R5U
  • Tryptophan operon repressor/operator complex [Escherichia coli (bacteria)]: PDB:1TRO
  • Argonaute (RNA interference protein) [Pyrococcus furiosus DSM 3638 (archaea, thermophile)]: PDB:1U04
  • Trp RNA-Binding Attenuation Protein in Complex with L-Tryptophan [Bacillus subtilis]: PDB:1WAP
  • Murine CAR nuclear receptor/inverse agonist androstenol complex [Mus musculus (house mouse)]: PDB:1XNX
  • Nuclear receptor mSF-1 LBD complexed with PG(ligand) [mouse]: PDB:1YMT
  • Ligand-binding domain of human nuclear receptor liver receptor homolog 1 (hLRH-1) in complex with the NR box 1 motif of human SHP [Homo sapiens (human)]: PDB:1YUC
  • DNA binding domain of human liver receptor homologue(hLRH-1 DBD) in Complex with dsDNA [Homo sapiens (human)]: PDB:2A66
  • mRNA decapping enzyme Dcp2p [Schizosaccharomyces pombe]: PDB:2A6T
  • DNA-dependent RNA polymerase / tagetitoxin complex [Thermus thermophilus (thermophile, bacteria)]: PDB:2BE5
  • A Piwi domain (part of RNAi protein argonaut)/siRNA-like duplex complex [Archaeoglobus fulgidus]: PDB:2BGG
  • Ribonuclease inhibitor (RI) [Sus scrofa (pig)]: PDB:2BNH
  • Lipoate protein ligase A (LplA) [Thermoplasma acidophilum (archaea,thermophile)]: PDB:2C8M
  • Cbf5-Nop10-Gar1 complex (part of the pseudouridylation enzyme) [Pyrococcus furiosus (thermophile, archaea)]: PDB:2EY4
  • RNase III (D44N) complexed with double-stranded RNA [Aquifex aeolicus (bacteria,thermophile)]: PDB:2EZ6
  • BPTF PHD finger-linker-bromodomain bound to H3K4me3 [Homo sapiens (human)]: PDB:2F6J
  • Dicer [Giardia intestinalis (flagellate)]: PDB:2FFL
  • Transcription regulating factor CSL-Notch-Mastermind/DNA complex [Caenorhabditis elegans (nematode)]: PDB:2FO1
  • Thiamine pyrophosphate-specific riboswitch [Escherichia coli (bacteria)]: PDB:2GDI
  • S-adenosylmethionine riboswitch [Thermoanaerobacter tengcongensis]: PDB:2GIS
  • Lysine-Specific Demethylase-1 [Homo sapiens (human)]: PDB:2H94
  • CIA-histone H3-H4 complex [Homo sapiens (human)]: PDB:2IO5
  • Exon Junction Complex [Human]: PDB:2J0S
  • Retinoic acid receptor-gamma / retinoic acid complex [Homo sapiens (human)]: PDB:2LBD
  • Trapped UBL activation complex [Human]: PDB:2NVU
  • Inositol-requiring protein-1 [Yeast]: PDB:2RIO

Globin protein

  • Myoglobin [Sperm whale]: PDB:1MBN
  • Oxidized alpha haemoglobin bound to alpha-haemoglobin-stabilizing protein (AHSP) [Homo sapiens (human)]: PDB:1Z8U

Others

  • Immunoglobulin M rheumatoid factor Fab complexed with IgG4 Fc [Homo sapiens (human)]: PDB:1ADQ
  • Complex between T-cell receptor, viral peptide and HLA-A2 [Homo sapiens (human)]: PDB:1AO7
  • Actin/DNase I complex [Oryctolagus cuniculus (European rabbit)]: PDB:1ATN
  • Myosin heavy chain [Argopecten irradians (bay scallop)]: PDB:1B7T
  • Clathrin heavy chain [Bos taurus (bovine)]: PDB:1B89
  • FOOT-AND-MOUTH DISEASE VIRUS [foot-and-mouth disease virus (FMDV)]: PDB:1BBT
  • COAGULATION FACTOR IX-BINDING PROTEIN A [Trimeresurus flavoviridis(habu snake)]: PDB:1BJ3
  • Collagen like model peptide (T3-785 peptide) [Synthetic peptide (containing human type III collagen sequence)]: PDB:1BKV
  • KcsA Potassium channel [Streptomyces lividans (bacteria)]: PDB:1BL8
  • Verotoxin-1 [Escherichia coli (bacteria)]: PDB:1BOV
  • Retinol binding protein [Homo sapiens (human)]: PDB:1BRP
  • Dethiobiotin synthase [Escherichia coli (bacteria)]: PDB:1BYI
  • Collagen-like peptide [Homo sapiens (human)?]: PDB:1CAG
  • SCAFFOLDING PROTEIN GPD [bacteriophage phiX174]: PDB:1CD3
  • TATA binding protein (TBP)/DNA complex [Homo sapiens (human)]: PDB:1CDW
  • Calmodulin [Homo sapiens (human)]: PDB:1CLL
  • Prostaglandin H2 synthase-1 complex with flurbiprofen [Ovis aries (sheep)]: PDB:1CQE
  • Crambin [Crambe abyssinica (Abyssinian cabbage)]: PDB:1CRN
  • Axonin-1 (N-terminal domain) [Gallus gallus (chicken)]: PDB:1CS6
  • Transferrin (iron transport protein) receptor (TfR) protein [Homo sapiens (human)]: PDB:1CX8
  • Apoptosis-inducing ligand 2 (Apo2L,TRAIL)/death receptor 5 (DR5) complex [Homo sapiens (human)]: PDB:1D0G
  • Coagulation factor VIII precursor [Homo sapiens (human)]: PDB:1D7P
  • Major prion protein 1 precursor [Bos taurus (bovine)]: PDB:1DX0
  • E-cadherin [Mus musculus (house mouse)]: PDB:1EDH
  • Green fluorescent protein [Aequorea victoria (jellyfish)]: PDB:1EMA
  • Botulinum neurotoxin type B [Clostridium botulinum (bacteria)]: PDB:1EPW
  • Bone morphogenetic protein 2 (BMP2)/BRIA ectodomain complex [Homo sapiens (human)]: PDB:1ES7
  • Botulinum neurotoxin type B complex with sialyllactose [Clostridium botulinum (bacteria)]: PDB:1F31
  • Rhodopsin [Bos taurus (Bovine)]: PDB:1F88
  • ImmunoglobulinG1-kappa Fab D1.3 (light chain) [Mus musculus (house mouse)]: PDB:1FDL
  • Ferritin (iron transport protein) H-chain mutant (LYS 86 replaced by GLN) [Homo sapiens (human)]: PDB:1FHA
  • Immunosuppressant drug (FK506) binding protein [Homo sapiens (human)]: PDB:1FKF
  • Botulinum neurotoxin type B complex with zinc ion and inhibitor (bis(5-amidino-2-benzimidazolyl)methane) [Clostridium botulinum (bacteria)]: PDB:1G9B
  • ENVELOPE PROTEIN GP120 [Human Immunodeficiency Virus type 1]: PDB:1GC1
  • NAD(P)H:quinone oxidoreductase 1 [Homo sapiens (human)]: PDB:1GG5
  • Crustacyanin [Homarus gammarus (European lobster)]: PDB:1GKA
  • Iron transport protein Serotransferrin (serum transferrin) [Sus scrofa (pig)]: PDB:1H76
  • Biphenyl-2,3-diol 1,2-dioxygenase [Burkholderia cepacia (bacteria)]: PDB:1HAN
  • Human leukocyte antigen B27 [Homo sapiens (human)]: PDB:1HSA
  • Immunoglobulin IgG2A [Mus musculus (house mouse)]: PDB:1IGT
  • COAGULATION FACTOR X BINDING PROTEIN [Homo sapiens (human)]: PDB:1IOD
  • INFLUENZA A SUBTYPE N2 NEURAMINIDASE [influenza virus]: PDB:1IVD
  • Multidrug efflux transporter AcrB [Escherichia coli (bacteria)]: PDB:1IWG
  • Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 [Oryctolagus cuniculus (rabbit)]: PDB:1IWO
  • human cardiac troponin in the Ca2+-saturated form [Homo sapiens (human)]: PDB:1J1D
  • Complex of ADP-ribosylation factor 1 and ADP-ribosylation factor binding protein GGA1 [Mus musculus (house mouse)]: PDB:1J2J
  • Aquaporin 1 water channel [Bos taurus (bovine)]: PDB:1J4N
  • anthrax lethal factor [Bacillus anthracis(anthrax)]: PDB:1J7N
  • Trp-cage designed protein TC5b [N/A (synthetic)]: PDB:1L2Y
  • Luciferase [Photinus pyralis (north american firefly)]: PDB:1LCI
  • Ca-activated K+ channel [Methanothermobacter thermautotrophicus (archaea)]: PDB:1LNQ
  • LDL receptor-binding domain of Apolipoprotein E3 [Homo sapiens (human)]: PDB:1LPE
  • Complex of acetylcholinesterase and fasciculin 2 [Mus musculus (house mouse) / Dendroaspis angusticeps (eastern green mamba)]: PDB:1MAH
  • Apoptosis inhibitor BCL-XL [Homo sapiens (human)]: PDB:1MAZ
  • Camel single-domain VH antibody complexed with lysozyme [Camelus dromedarius (camel)]: PDB:1MEL
  • Human LDL receptor (extracellular domain) [Homo sapiens (human)]: PDB:1N7D
  • Lysyl oxidase [Pichia pastoris]: PDB:1N9E
  • Neural-cadherin (N-cadherin) [Mus musculus (house mouse)]: PDB:1NCI
  • Nucleoside diphosphate (NDP) kinase [Dictyostelium discoideum (slime mold) P105G mutant]: PDB:1NCL
  • Hemeoxygenase domain of cytokine-inducible nitric oxide syntase [Mouse]: PDB:1NOS
  • KvAP, a voltage-dependent K+ channel [Aeropyrum pernix (archaea)]: PDB:1ORQ
  • B-cell-activating factor (BAFF)/BAFF recepter (BAFF-R) complex [Homo sapiens (human)]: PDB:1OTZ
  • Inward rectifier potassium channel KirBac1.1 [Burkholderia pseudomallei (bacteria)]: PDB:1P7B
  • Phosphoporin [Escherichia coli (bacteria)]: PDB:1PHO
  • Penicillin acylase [Escherichia coli (bacteria)]: PDB:1PNL
  • C-H-RAS P21 protein catalytic domain (wild type) [Homo sapiens (human)]: PDB:1Q21
  • Major prion protein precursor [Homo sapiens (human)]: PDB:1QLX
  • Interferon alpha 2B [Homo sapiens (human)]: PDB:1RH2
  • Protein conducting channel secY/secG/secE complex [Methanococcus jannaschii (archaea)]: PDB:1RH5
  • SRP/SRP receptor complex [Thermus aquaticus (bacteria)]: PDB:1RJ9
  • Sialyltransferase CstII/CMP-NeuAc complex [Campylobacter jejuni (bacteria)]: PDB:1RO7
  • Nerve growth factor in complex with its receptor, p75 [Homo sapiens (human)]: PDB:1SG1
  • Periplasmic chaperone Skp [Escherichia coli (bacteria)]: PDB:1SG2
  • VP4 spike-like protein of rotavirus [Rotavirus]: PDB:1SLQ
  • Water channel aquaporin-0 [Ovis aries (sheep)]: PDB:1SOR
  • Superoxide dismutase [Homo sapiens (human)]: PDB:1SPD
  • Long-chain fatty acid transporter (FadL) [Escherichia coli (bacteria)]: PDB:1T16
  • Rab5 complex with Rabaptin5 C-terminal Domain [Homo sapiens (human)]: PDB:1TU3
  • Integrin/cacodylate ion complex [Homo sapiens (human)]: PDB:1TYE
  • ESCRT-II complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1U5T
  • Phosphodiesterase 5 [Homo sapiens (human)]: PDB:1UDT
  • Serum albumin precursor [Homo sapiens (human)]: PDB:1UOR
  • Amphiphysin BAR domain [Drosophila melanogaster (fruit fly)]: PDB:1URU
  • Mycobacterial membrane protein, main porin (MspA) [Mycobacterium smegmatis (bacteria)]: PDB:1UUN
  • Artificial nucleotide-binding protein (ANBP) in a complex with bound ADP [N/A (synthetic)]: PDB:1UW1
  • Polysialic acid-degrading endosialidase [Bacteriophage K1F]: PDB:1V0E
  • Calcium Pump with a bound ATP analogue [Oryctolagus cuniculus (rabbit)]: PDB:1VFP
  • Vanadium-containing chloroperoxidase (CPO) [Curvularia inaequalis]: PDB:1VNC
  • RNA packing motor protain [Pseudomonas phage PHI12]: PDB:1W44
  • Glycolipid transfer protein GLTP [Bos taurus (bovine)]: PDB:1WBE
  • Adenylyl Cyclase in complex with alpha,beta-methylene-ATP [Spirulina platensis (cyanobacteria)]: PDB:1WC0
  • Bet3 in Golgi localization of tethering factor TRAPP [Mus musculus (house mouse)]: PDB:1WC8
  • Antimicrobial peptide, nisin, comoplexed with lipid II [Lactococcus lactis (lactic acid bacteria)]: PDB:1WCO
  • Antifreeze protein isoform hplc6 [Pseudopleuronectes americanus (winter flounder)]: PDB:1WFB
  • Archaeal toxin-antitoxin RelB-RelE complex [Pyrococcus horikoshii (archaea, thermophile)]: PDB:1WMI
  • Glutamate transporter homolog [Pyrococcus horikoshii OT3 (archaea)]: PDB:1XFH
  • Bacterial sensory rhodopsin [Anabaena sp. (cyanobacteria)]: PDB:1XIO
  • N-terminal Domain of Nucleoporin Nup159 [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1XIP
  • Cholera toxin [Vibrio cholerae]: PDB:1XTC
  • Bni1p Formin Homology 2 (FH2) Domain complexed with ATP-actin [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1Y64
  • Peptide segment GNNQQNY from Sup35 forming amyloid-like fibrils [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1YJP
  • gamma-delta T cell receptor in complex with MHC T22 [Mus musculus (house mouse)]: PDB:1YPZ
  • Apoptotic protease-activating factor 1 with ADP [Homo sapiens (human)]: PDB:1Z6T
  • Aromatic prenyltransferase Orf2 [Streptomyces sp. strain CL190 (bacteria)]: PDB:1ZB6
  • Na(+)/H(+) antiporter [Escherichia coli (bacteria)]: PDB:1ZCD
  • Hepatitis C virus replicase NS5A [Hepatitis C virus(HCV) ]: PDB:1ZH1
  • Toll-like receptor 3 (TLR3) extracellular domain (ECD) [Homo sapiens (human)]: PDB:1ZIW
  • Potassium-channel KcsA [Streptomyces lividans (actinobacteria)]: PDB:1ZWI
  • Integron integrase-attC sequence complex [Vibria cholelae]: PDB:2A3V
  • Bacterial homolog of Na+/Cl- dependent neurotransmitter transporters [Aquifex aeolicus (thermophile, bacteria) VF5]: PDB:2A65
  • NaK channel [Bacillus cereus]: PDB:2AHY
  • quorum-sensing protein SdiA [bacteria (E.coli)]: PDB:2AVX
  • CorA Mg2+ transporter [Thermotoga maritima (bacteria, thermophile)]: PDB:2BBJ
  • Filamin A complexed with integrin beta 7 tail fragment [Homo sapiens (human)]: PDB:2BRQ
  • Rabex-5/ubiquitin complex [Homo sapiens (human)]: PDB:2C7N
  • ZEBRA protein complexed with double strand DNA [Epstein-Barr virus (EBV, Human herpesvirus 4 (HHV-4))]: PDB:2C9L
  • SARS coronavirus ORF-9b protein [Human severe acute respiratory syndrome (SARS) virus]: PDB:2CME
  • Cytochrome c peroxidase [Saccharomyces cerevisiae (Baker's yeast)]: PDB:2CYP
  • Myosin V complexed with calmodulins [Gallus gallus (chicken)]: PDB:2DFS
  • Periplasmic binding protein [Bordetella pertussis Tohama I (bacteria)]: PDB:2F5X
  • Beta-2-microglobulin [Homo sapiens (human)]: PDB:2F8O
  • Urokinase plasminogen activator (uPA) complexed with it's soluble receptor (suPAR) and the antibody against the receptor (ATN615) [uPA,suPAR:Homo sapiens (human) / ATN615:Mus musculus (mouse)]: PDB:2FD6
  • Ta0583, an archaeal actin homolog [Thermoplasma acidophilum (archaea,thermophile)]: PDB:2FSN
  • Mitochondrial import receptor TOM70 [Saccharomyces cerevisiae (yeast)]: PDB:2GW1
  • Tie2 receptor ectodomain complexed with Ang2 [Human]: PDB:2GY7
  • Rab11/FIP2(RBD domain) complex [Human]: PDB:2GZD
  • Complex of integrin B-subunit cytoplasmic domain and talin F3 domain [Gallus gallus domesticus(chicken)]: PDB:2H7E
  • ABC transporters Sav1866 [S. aureus]: PDB:2HYD
  • Apoptosis regulator, Bcl-2 homologous antagonist/killer(BAK) [Human]: PDB:2IMS
  • Lysozyme [Gallus gallus (chicken)]: PDB:2LYZ
  • HIV-1 enverope protein gp120/b12 complex [Human]: PDB:2NY7
  • Mechanosensitive ion channel [Mycobacterium tuberculosis (bacteria)]: PDB:2OAR
  • Outer membrane porin D2 (OprD) [Pseudomonas aeruginos]: PDB:2ODJ
  • ABC transporter ModBC in complex with its binding protein ModA [Archaeoglobus fulgidus (archaea, thermophile)]: PDB:2ONK
  • Transport vesicle coat protein, Sec13/31 complex [Yeast]: PDB:2PM7
  • C-H-RAS P21 protein catalytic domain (oncogenic G12V) [Homo sapiens (human)]: PDB:2Q21
  • Acid sensing ion channel, ASIC1 [Chicken]: PDB:2QTS
  • Salmonella effector protein SopA [Salmonella bacterium]: PDB:2QYU
  • Paddle-chimaera K+ channel [Rat]: PDB:2R9R
  • Outer membrane component of bacteria drug efflux pump, TolC [E.coli]: PDB:2VDD
  • IS608 transposase TnpA / DNA complex [Helicobacter pylori]: PDB:2VJV
  • Toll-like receptor1 (TLR1)/TLR2/lipopeptide complex [Homo sapiens (human)]: PDB:2Z7X
  • Sarcoplasmic reticulum calcium pump [Oryctolagus cuniculus (rabbit)]: PDB:2ZBD
  • E. coli DNA polymerase III, beta-subunit / DNA complex [Escherichia coli]: PDB:3BEP
  • Sec13-Nup145C hetero-octamer [human (Sec13), yeast (Nup145C)]: PDB:3BG0
  • Beta-lactamase [Bacillus licheniformis (bacteria)]: PDB:4BLM
  • Human rhinovirus 14 coat protein [Human rhinovirus 14 (human common cold virus)]: PDB:4RHV
  • Cisplatin/DNA complex [N/A]: PDB:5BNA