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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P12259 New Search
17PDB entries
22Biological assembly
30chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1CZS CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: COMPLEX WITH PHENYLMERCURY Deposited 1999-09-07 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 2065–2224（160 aa） Fragment：C2 DISCOIDIN-LIKE DOMAIN
Not recorded PHG PHENYLMERCURY × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.2；AMMONIUM SULFATE, pH 10.20, VAPOR DIFFUSION, HANGING DROP
Resolution 1.90 Å R-free 0.258
1CZT CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V Deposited 1999-09-07 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 2065–2224（160 aa） Fragment：C2 DISCOIDIN-LIKE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.2；AMMONIUM SULFATE, pH 10.20, VAPOR DIFFUSION, HANGING DROP
Resolution 1.87 Å R-free 0.242
1CZV CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: DIMERIC CRYSTAL FORM Deposited 1999-09-07 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 2065–2224（160 aa） Fragment：C2 DISCOIDIN-LIKE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 10；pH 10.00
Resolution 2.40 Å R-free 0.257
1CZV CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: DIMERIC CRYSTAL FORM Deposited 1999-09-07 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 2065–2224（160 aa） Fragment：C2 DISCOIDIN-LIKE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 10；pH 10.00
Resolution 2.40 Å R-free 0.257
3P6Z Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 685–737（53 aa） Fragment：FACTOR V, A2-B DOMAIN LINKER
Not recorded NA SODIUM ION × 3 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 30 mM Ca2+, 30 mM Mg2+, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.239
3P6Z Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain I 685–737（53 aa） Fragment：FACTOR V, A2-B DOMAIN LINKER
Not recorded NA SODIUM ION × 6 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 30 mM Ca2+, 30 mM Mg2+, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.239
3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain M 685–737（53 aa） Fragment：FACTOR V, A2-B DOMAIN LINKER
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BEN BENZAMIDINE × 1 NA SODIUM ION × 2 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.55 Å R-free 0.279
3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain N 685–737（53 aa） Fragment：FACTOR V, A2-B DOMAIN LINKER
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BEN BENZAMIDINE × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.55 Å R-free 0.279
3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain O 685–737（53 aa） Fragment：FACTOR V, A2-B DOMAIN LINKER
Not recorded BEN BENZAMIDINE × 1 NA SODIUM ION × 1 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.55 Å R-free 0.279
3P70 Structural basis of thrombin-mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction Deposited 2010-10-11 Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain P 685–737（53 aa） Fragment：FACTOR V, A2-B DOMAIN LINKER
Not recorded BEN BENZAMIDINE × 1 NA SODIUM ION × 2 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM MOPS/HEPES-Na, pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methylpentane-2,4-diol (MPD), 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.55 Å R-free 0.279
3S9C Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor V Deposited 2011-06-01 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1561–1574（14 aa） Fragment：UNP residues 1561-1574
Not recorded BGC beta-D-glucopyranose × 1 GLC alpha-D-glucopyranose × 1 ACT ACETATE ION × 4 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；20% PEG 3350, 0.2M zinc acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.218
7KVE Cryo-EM structure of human Factor V at 3.3 Angstrom resolution Deposited 2020-11-27 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 29–2224（2196 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7KVF Cryo-EM structure of human Factor V at 3.6 Angstrom resolution Deposited 2020-11-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 29–2224（2196 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7KXY Cryo-EM structure of human Factor Va at 4.4 Angstrom resolution Deposited 2020-12-05 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 29–737（709 aa） Fragment：UNP residues 29-737
Chain B 1574–2224（651 aa） Fragment：UNP residues 1574-2224
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7TPP Cryo-em structure of human prothrombin:prothrombinase at 4.1 Angstrom resolution Deposited 2022-01-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain C 29–737（709 aa） Fragment：domains A1 and A2 (UNP residues 29-737)
Chain D 1574–2224（651 aa） Fragment：domains C1, C2, and A3 (UNP residues 1574-2224)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20mM Hepes, 150mM NaCl, 5mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8FDG Cryo-EM structure of coagulation factor V short Deposited 2022-12-03 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 29–783（755 aa）
Chain A 1487–2224（738 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；2 second blot 20 second wait time
Resolution 3.20 Å
8TN9 Structural architecture of the acidic region of the B domain of coagulation factor V Deposited 2023-08-01 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 29–2224（2196 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9CTH Preliminary map of the Prothrombin-prothrombinase complex on nano discs Deposited 2024-07-25 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain A 29–737（709 aa） Fragment：Domains A1 and A2 (UNP residues 29-737)
Chain E 1574–2224（651 aa） Fragment：Domains C1, C2, and A3 (UNP residues 1574-2224)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, and 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.47 Å
9I2H A 3.3 angstrom cryo-EM structure of an engineered high-affinity human prothrombinase complex Deposited 2025-01-20 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: pentameric（5） Review required
Chain A 29–737（709 aa）
Chain B 1574–2224（651 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 NA SODIUM ION × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM HEPES, 150mM NaCl and 5mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9MOT Cryo-EM structure of factor Va bound to activated protein C Deposited 2024-12-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 29–737（709 aa） Fragment：Domains A1 and A2 (UNP residues 29-737)
Chain B 1574–2224（651 aa） Fragment：Domains C1, C2, and A3 (UNP residues 1574-2224)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2, 40uM n-Dodecyl-B-D-Maltoside
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9MOV Cryo-EM structure of factor Va bound to activated protein C Deposited 2024-12-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 29–737（709 aa） Fragment：Domains A1 and A2 (UNP residues 29-737)
Chain B 1574–2224（651 aa） Fragment：Domains C1, C2, and A3 (UNP residues 1574-2224)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2, 40uM n-Dodecyl-B-D-Maltoside
cryo-EM buffer pH 7.4；20 mM HEPES, 150 mM NaCl, 5 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9YQ8 Cryo-EM complex of meizothrombinDESF1, factor Xa, and factor Va Deposited 2025-10-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain A 1574–2224（651 aa） Fragment：Domains C1, C2, and A3 (UNP residues 1574-2224)
Chain B 29–702（674 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.