Enzymes
- Alcohol dehydrogenase class IV sigma chain [Homo sapiens (human)]: PDB:1D1S
- 3-isopropylmalate dehydrogenase [Thermus thermophilus (bacteria,thermophile)]: PDB:1IPD
- Vanadium-containing chloroperoxidase (CPO) [Curvularia inaequalis]: PDB:1VNC
- Cytochrome c peroxidase [Saccharomyces cerevisiae (Baker's yeast)]: PDB:2CYP
- Biphenyl-2,3-diol 1,2-dioxygenase [Burkholderia cepacia (bacteria)]: PDB:1HAN
- Luciferase [Photinus pyralis (north american firefly)]: PDB:1LCI
- Superoxide dismutase [Homo sapiens (human)]: PDB:1SPD
- Ribonucleotide reductase [Escherichia coli (bacteria)]: PDB:1MXR
- Pyruvate dehydrogenase complex [Geobacillus stearothermophilus (bacteria,thermophile)]: PDB:1W85
- deoxyribonucleic acid (DNA) [N/A (synthetic)]: PDB:1BNA
- Tryptophan operon repressor/operator complex [Escherichia coli (bacteria)]: PDB:1TRO
- Complex of (Arginyl-tRNA synthetase/tRNA/Arginine) [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1F7U
- DNA-DIRECTED RNA POLYMERASE II [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1I6H
- DNA repair enzyme [Homo sapiens (human)]: PDB:1EWN
- TAQ polymerase (DNA synthesizer)/DNA complex [Thermus aquaticus (bacteria)]: PDB:1TAU
- 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
- Transcriptional activator GCN4/DNA complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1YSA
- The zinc finger (DNA binding site) of transcription factor Zif268/DNA complex [Mus musculus (house mouse)]: PDB:1ZAA
- Ribosome recycling factor (RRF) [Thermotoga maritima (thermophile, bacteria)]: PDB:1DD5
- Eukaryotic protein Release Factor eRF1 [Homo sapiens (human)]: PDB:1DT9
- Replication terminator protein(Tus)/DNA complex [Escherichia coli]: PDB:1ECR
- Transcription factor c-Fos-c-Jun / DNA complex [Homo sapiens (Human)]: PDB:1FOS
- 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
- 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
- RNA polymerase II-transcribing complex in the post-translocation state [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1SFO
- clamp loader (RFC) bound to the DNA sliding clamp (PCNA) [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1SXJ
- Group I self-splicing intron in complex with its exons [Homo sapiens (Human)]: PDB:1U6B
- Argonaute (RNA interference protein) [Pyrococcus furiosus DSM 3638 (archaea, thermophile)]: PDB:1U04
- Human Argonaute2 to form minimal RISC [Pyrococcus furiosus (archaea)]: PDB:1Z25
- DNA repairing complex RecBCD [Escherichia coli (bacteria)]: PDB:1W36
- RNA packing motor protain [Pseudomonas phage PHI12]: PDB:1W44
- Human Telomeric DNA (monomer with 22 bases) [Homo sapiens (human)]: PDB:1KF1
- SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54 [Danio rerio (zebra fish)]: PDB:1Z3I
- A Piwi domain (part of RNAi protein argonaut)/siRNA-like duplex complex [Archaeoglobus fulgidus]: PDB:2BGG
- E. coli DNA polymerase III, beta-subunit [Escherichia coli (bacteria)]: PDB:2POL
- E. coli DNA polymerase III, beta-subunit / DNA complex [Escherichia coli]: PDB:3BEP
- Sex-lethal (Sxl) protein/RNA complex [Drosophila melanogaster (fruit fly)]: PDB:1B7F
- Restriction endonuclease BamHI/DNA complex [Bacillus amyloliquefaciens (bacteria)]: PDB:1BHM
- 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
- human 8-oxoguanine glycosylase (hOGG1) bound to DNA [Homo sapiens (human)]: PDB:1EBM
- Mammalian Poly(A) Polymerase [Bos taurus (bovine)]: PDB:1F5A
- lac repressor [Escherichia coli (bacteria)]: PDB:1LBI
- Deoxyribodipyrimidine photolyase/DNA complex [Synechococcus sp. PCC 6301 (cyanobacteria)]: PDB:1TEZ
- XPD helicase [Sulfolobus acidocaldarius]: PDB:3CRV
- SR (serine/arginine rich) protein kinase SRPK1 / peptide complex [Homo sapiens (human)]: PDB:1WBP
- Intein PI-SceI homing endonuclease [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1DFA
- Intein PI-SceI homing endonuclease / DNA complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1LWS
- YibK methyltransferase (knot protein) complexed with an inhibitor (AdoHcy) [Haemophilus influenzae (bacteria)]: PDB:1MXI
- Hypothetical RNA 2'-O-ribose methyltransferase (RrmA) [Thermus thermophilus (bacteria)]: PDB:1IPA
- 5-methyluridine methyltransferase TrmA [Escherichia coli]: PDB:3BT7
- Phage twort group I ribozyme (self-splicing intron) complexed with it's product [Bacteriophage Twort (virus)]: PDB:1Y0Q
- CCA-adding enzyme [Archaeoglobus fulgidus (Archaea)]: PDB:1UET
- Histon modification protein WRD5 / histon subunit H3 complex [Human]: PDB:2H13
- Ftsk(C-domain) hexmer [Bacteria(Pseudomonas-aeruginosa)]: PDB:2IUU
- Protein phosphatase 2A (heterotrimeric holoenzyme) [Homo sapiens (human) ]: PDB:2IAE
- Glutamate decarboxylase 1(GAD) / cofactor PLP complexed [human]: PDB:2OKJ
Virus
- HIV-1 enverope protein gp120/b12 complex [Human]: PDB:2NY7
- Salmonella effector protein SopA [Salmonella bacterium]: PDB:2QYU
Cancer related
- C-H-RAS P21 protein catalytic domain (wild type) [Homo sapiens (human)]: PDB:1Q21
- C-H-RAS P21 protein catalytic domain (oncogenic G12V) [Homo sapiens (human)]: PDB:2Q21
- NAD(P)H:quinone oxidoreductase 1 [Homo sapiens (human)]: PDB:1GG5
- Interleukin-18 [Homo sapiens (human)]: PDB:1J0S
- Cisplatin/DNA complex [N/A]: PDB:5BNA
- SV40 large tumor antigen [Simian virus 40 (virus)]: PDB:1SVM
- 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
- Arginases I and nor-NOHA complex [Rattus norvegicus (rat)]: PDB:1HQH
- Nicotinamide phosphoribosyltransferase (NMPRTase): Complex with FK866 [Human]: PDB:2GVJ
Plant proteins
- Light harvesting protein B-800/850 [Rhodopseudomonas acidophila (phototrophic bacteria)]: PDB:1KZU
- Photosystem I P700 chlorophyll a apoprotein A1 [Synechococcus elongatus (cyanobacteria)]: PDB:1JB0
- Photosystem II [Synechococcus elongatus (cyanobacteria)]: PDB:1FE1
- Photosynthetic Reaction Center [Rhodopseudomonas viridis (phototrophic bacteria)]: PDB:1PRC
- Nitrogenase molybdenum iron protein [Azotobacter vinelandii (aerobic nitrogen-fixing bacteria)]: PDB:3MIN
- Papain [Carica papaya (Papaya)]: PDB:9PAP
- Crambin [Crambe abyssinica (Abyssinian cabbage)]: PDB:1CRN
- Cyanobacterial photosystem II [Thermosynechococcus elongatus (cyanobacteria)]: PDB:1S5L
- light-harvesting complex of photosystem II (LHC-II) [Spinacia oleracea (Spinach) ]: PDB:1RWT
- Cytochrome b6f complex [Mastigocladus laminosus (cyanobacteria)]: PDB:1VF5
- Archaeal Rrp4 Exosomes [Archaeoglobus fulgidus (archaea)]: PDB:2BA0
Movement
- Myosin heavy chain [Argopecten irradians (bay scallop)]: PDB:1B7T
- Actin/DNase I complex [Oryctolagus cuniculus (European rabbit)]: PDB:1ATN
- human cardiac troponin in the Ca2+-saturated form [Homo sapiens (human)]: PDB:1J1D
- Bni1p Formin Homology 2 (FH2) Domain complexed with ATP-actin [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1Y64
- Ta0583, an archaeal actin homolog [Thermoplasma acidophilum (archaea,thermophile)]: PDB:2FSN
Drug target
- Prostaglandin H2 synthase-1 complex with flurbiprofen [Ovis aries (sheep)]: PDB:1CQE
- Beta-lactamase [Bacillus licheniformis (bacteria)]: PDB:4BLM
- beta-secretase 2 (BACE2) [Homo sapiens (human)]: PDB:2EWY
- Nicotinamide phosphoribosyltransferase (NMPRTase) [Human]: PDB:2GVG
Protein folding
- Chaperonin (GroEL-GroES) / ADP complex [Escherichia coli (bacteria)]: PDB:1AON
- Thiol:disulfide interchange protein DsbC [Escherichia coli (bacteria)]: PDB:1EEJ
- Heat shock protein HSP33 [Escherichia coli (bacteria)]: PDB:1HW7
- Heat shock protein Hsc70/Hsp110 complex [Bovine/Yeast]: PDB:3C7N
- Flavoenzyme Ero1p [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1RP4
- Periplasmic chaperone Skp [Escherichia coli (bacteria)]: PDB:1SG2
- Ribosomal chaperon trigger factor complexed with 50S ribosome [Escherichia coli (bacteria)]: PDB:1W26
- Trp-cage designed protein TC5b [N/A (synthetic)]: PDB:1L2Y
Oxygen Transport and Storage
Hormones, Cytokines, and Receptors
- Insulin [Sus scrofa (pig)]: PDB:4INS
- Interferon alpha 2B [Homo sapiens (human)]: PDB:1RH2
- Interleukin-1 beta [Homo sapiens (human)]: PDB:1I1B
- Growth hormon complexed with its receptor [Homo sapiens (human)]: PDB:3HHR
- Androgen receptor [Homo sapiens (human)]: PDB:1E3G
- Bone morphogenetic protein 2 (BMP2)/BRIA ectodomain complex [Homo sapiens (human)]: PDB:1ES7
- Human LDL receptor (extracellular domain) [Homo sapiens (human)]: PDB:1N7D
- Acetylcholine Receptor [Torpedo californica]: PDB:1OED
- Retinoic acid receptor-gamma / retinoic acid complex [Homo sapiens (human)]: PDB:2LBD
- B-cell-activating factor (BAFF)/BAFF recepter (BAFF-R) complex [Homo sapiens (human)]: PDB:1OTZ
- GM-CSF/GM-CSF receptor complex [Homo sapiens]: PDB:3CXE
Cell regulation and Apotosis
- Cyclin A/cyclin-dependent kinase 2(CDK-2) complex [Homo sapiens (human)]: PDB:1FIN
- Interleukin-1beta converting enzyme(ICE)/inhibitor peptide complex [Homo sapiens (human)]: PDB:1IBC
- Apoptosis inhibitor BCL-XL [Homo sapiens (human)]: PDB:1MAZ
- Tyrosine-protein kinase c-Src/AMP-PNP complex [Homo sapiens (human)]: PDB:2SRC
- Sialyltransferase CstII/CMP-NeuAc complex [Campylobacter jejuni (bacteria)]: PDB:1RO7
- Integrin/cacodylate ion complex [Homo sapiens (human)]: PDB:1TYE
- Apoptotic protease-activating factor 1 with ADP [Homo sapiens (human)]: PDB:1Z6T
- Axonin-1 (N-terminal domain) [Gallus gallus (chicken)]: PDB:1CS6
- Apoptosis-inducing ligand 2 (Apo2L,TRAIL)/death receptor 5 (DR5) complex [Homo sapiens (human)]: PDB:1D0G
- Rabex-5/ubiquitin complex [Homo sapiens (human)]: PDB:2C7N
- Complex of integrin B-subunit cytoplasmic domain and talin F3 domain [Gallus gallus domesticus(chicken)]: PDB:2H7E
- Inositol-requiring protein-1 [Yeast]: PDB:2RIO
Metal transporters, Pumps, and Channels
- Iron transport protein Serotransferrin (serum transferrin) [Sus scrofa (pig)]: PDB:1H76
- Transferrin (iron transport protein) receptor (TfR) protein [Homo sapiens (human)]: PDB:1CX8
- Ferritin (iron transport protein) H-chain mutant (LYS 86 replaced by GLN) [Homo sapiens (human)]: PDB:1FHA
- Calmodulin [Homo sapiens (human)]: PDB:1CLL
- Ca-activated K+ channel [Methanothermobacter thermautotrophicus (archaea)]: PDB:1LNQ
- Mechanosensitive ion channel [Mycobacterium tuberculosis (bacteria)]: PDB:2OAR
- Water channel aquaporin-0 [Ovis aries (sheep)]: PDB:1SOR
- Calcium Pump with a bound ATP analogue [Oryctolagus cuniculus (rabbit)]: PDB:1VFP
- Sarcoplasmic reticulum calcium pump [Oryctolagus cuniculus (rabbit)]: PDB:2ZBD
- KcsA Potassium channel [Streptomyces lividans (bacteria)]: PDB:1BL8
- Aquaporin 1 water channel [Bos taurus (bovine)]: PDB:1J4N
- KvAP, a voltage-dependent K+ channel [Aeropyrum pernix (archaea)]: PDB:1ORQ
- Inward rectifier potassium channel KirBac1.1 [Burkholderia pseudomallei (bacteria)]: PDB:1P7B
- Potassium-channel KcsA [Streptomyces lividans (actinobacteria)]: PDB:1ZWI
- Phosphoporin [Escherichia coli (bacteria)]: PDB:1PHO
- Outer membrane porin D2 (OprD) [Pseudomonas aeruginos]: PDB:2ODJ
Material transport
- LDL receptor-binding domain of Apolipoprotein E3 [Homo sapiens (human)]: PDB:1LPE
- Alpha-thrombin/hirudin complex [Homo sapiens (human)/Hirudo medicinalis (leech)]: PDB:4HTC
- Clathrin heavy chain [Bos taurus (bovine)]: PDB:1B89
- Long-chain fatty acid transporter (FadL) [Escherichia coli (bacteria)]: PDB:1T16
- Serum albumin precursor [Homo sapiens (human)]: PDB:1UOR
- N-terminal Domain of Nucleoporin Nup159 [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1XIP
- Multidrug efflux transporter AcrB [Escherichia coli (bacteria)]: PDB:1IWG
- Glutamate transporter homolog [Pyrococcus horikoshii OT3 (archaea)]: PDB:1XFH
- Periplasmic binding protein [Bordetella pertussis Tohama I (bacteria)]: PDB:2F5X
- Amphiphysin BAR domain [Drosophila melanogaster (fruit fly)]: PDB:1URU
- ABC transporters Sav1866 [S. aureus]: PDB:2HYD
- Rab11/FIP2(RBD domain) complex [Human]: PDB:2GZD
Signaling
- Rhodopsin [Bos taurus (Bovine)]: PDB:1F88
- Protein kinase CheY/CheA complex (bacteria chemotaxis) [Escherichia coli (bacteria)]: PDB:1A0O
- DBL homology domain from beta-PIX [Homo sapiens (human)]: PDB:1BY1
- Ubiquitin ligase complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1LDD
- ESCRT-II complex [Saccharomyces cerevisiae (Baker's yeast)]: PDB:1U5T
- Fungal galectin CGL2 [Coprinopsis cinerea (Inky cap fungus)]: PDB:1UL9
- Bet3 in Golgi localization of tethering factor TRAPP [Mus musculus (house mouse)]: PDB:1WC8
- Bacterial sensory rhodopsin [Anabaena sp. (cyanobacteria)]: PDB:1XIO
- Murine CAR nuclear receptor/inverse agonist androstenol complex [Mus musculus (house mouse)]: PDB:1XNX
- Ubiquitin ligase(E6AP)/ubiquitin-conjugating enzyme(UbcH7) complex [Homo sapiens (human)]: PDB:1C4Z
- Arginases I and nor-NOHA complex [Rattus norvegicus (rat)]: PDB:1HQH
- Mitogen-activated protein (MAP) kinase ERK2 [Rattus norvegicus (rat)]: PDB:1ERK
- SRP/SRP receptor complex [Thermus aquaticus (bacteria)]: PDB:1RJ9
- 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
- Rab5 complex with Rabaptin5 C-terminal Domain [Homo sapiens (human)]: PDB:1TU3
- DNA binding domain of human liver receptor homologue(hLRH-1 DBD) in Complex with dsDNA [Homo sapiens (human)]: PDB:2A66
- Adenylyl Cyclase in complex with alpha,beta-methylene-ATP [Spirulina platensis (cyanobacteria)]: PDB:1WC0
- SUMO1-conjugated thymine DNA glycosylase [Homo sapiens (human)]: PDB:1WYW
- Transcription regulating factor CSL-Notch-Mastermind/DNA complex [Caenorhabditis elegans (nematode)]: PDB:2FO1
- Retinol binding protein [Homo sapiens (human)]: PDB:1BRP
- quorum-sensing protein SdiA [bacteria (E.coli)]: PDB:2AVX
- Nuclear receptor mSF-1 LBD complexed with PG(ligand) [mouse]: PDB:1YMT
Pigments and Luminescence
- Crustacyanin [Homarus gammarus (European lobster)]: PDB:1GKA
- Green fluorescent protein [Aequorea victoria (jellyfish)]: PDB:1EMA
Body maintenance and components
- E-cadherin [Mus musculus (house mouse)]: PDB:1EDH
- Neural-cadherin (N-cadherin) [Mus musculus (house mouse)]: PDB:1NCI
- Antifreeze protein isoform hplc6 [Pseudopleuronectes americanus (winter flounder)]: PDB:1WFB
- Coagulation factor VIII precursor [Homo sapiens (human)]: PDB:1D7P
- Collagen-like peptide [Homo sapiens (human)?]: PDB:1CAG
- Nerve growth factor in complex with its receptor, p75 [Homo sapiens (human)]: PDB:1SG1
- Gamma-B crystallin (eye lens components protein) [Bos taurus (Bovine)]: PDB:4GCR
- Tie2 receptor ectodomain complexed with Ang2 [Human]: PDB:2GY7
Artificially synthesized protein
- Trp-cage designed protein TC5b [N/A (synthetic)]: PDB:1L2Y
- Artificial nucleotide-binding protein (ANBP) in a complex with bound ADP [N/A (synthetic)]: PDB:1UW1
Others
Being written
- Gamma delta resolvase / DNA complex [Escherichia coli]: PDB:1GDT
- [Not available]: PDB:1J2J
- [Not available]: PDB:1MAH
- [Not available]: PDB:1Z7C
- [Not available]: PDB:2AJE
- [Not available]: PDB:2BRQ
- [Not available]: PDB:2BR4
- 3-ketoacyl-coA thiolase 2 [Arabidopsis thaliana (mouse-ear cress)]: PDB:2C7Y
- Transcription-repair coupling factor [Escherichia coli]: PDB:2EYQ
- Thiamine pyrophosphate-specific riboswitch [Escherichia coli (bacteria)]: PDB:2GDI
- S-adenosylmethionine riboswitch [Thermoanaerobacter tengcongensis]: PDB:2GIS
- Mitochondrial import receptor TOM70 [Saccharomyces cerevisiae (yeast)]: PDB:2GW1
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