SAXSdb — 9mot

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Coagulation factor Va heavy chain

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 29–737 Chain B； UniProt 1574–2224	Fragment：Domains A1 and A2 (UNP residues 29-737) Fragment：Domains C1, C2, and A3 (UNP residues 1574-2224)	Vitamin K-dependent protein C heavy chain × 1 （P04070） 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

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9MOT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CZS CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: COMPLEX WITH PHENYLMERCURY Deposited 1999-09-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	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	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	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	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: pentameric	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
9MOV Cryo-EM structure of factor Va bound to activated protein C Deposited 2024-12-27	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	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	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	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

16 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FA5_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–709； UniProt 29–737 Author chain B； PDBConstruct 1–651； UniProt 1574–2224

Vitamin K-dependent protein C heavy chain

Homo sapiens

UniProt P04070

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 212–451	Mutation：S360A	Coagulation factor Va heavy chain × 1 （P12259） Coagulation factor Va light chain × 1 （P12259） 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

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9MOT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AUT Human activated protein C Deposited 1996-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 212–461（250 aa） Chain L 84–197（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.7；0.1 M CITRATE, 20% ISOPROPANOL 2% PEG 20000 PH 4.7	Resolution 2.80 Å
1LQV Crystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C. Deposited 2002-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 43–75（33 aa） Fragment：Protein C Gla domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；peg 400, potassium chloride, magnesium chloride, calcium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.222
1LQV Crystal structure of the Endothelial protein C receptor with phospholipid in the groove in complex with Gla domain of protein C. Deposited 2002-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 43–75（33 aa） Fragment：Protein C Gla domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PTY PHOSPHATIDYLETHANOLAMINE × 1 CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；peg 400, potassium chloride, magnesium chloride, calcium chloride, hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.222
3F6U Crystal structure of human Activated Protein C (APC) complexed with PPACK Deposited 2008-11-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 212–451（240 aa） Fragment：UNP residues 212-451 Chain L 91–188（98 aa） Fragment：UNP residues 91-188	Not recorded	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 NA SODIUM ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.236
3JTC Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins Deposited 2009-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 43–75（33 aa） Fragment：GLA domain (UNP residues 43-75)	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PTY PHOSPHATIDYLETHANOLAMINE × 1 MG MAGNESIUM ION × 2 CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；PEG 400, potassium chloride, magnesium chloride, calcium chloride, HEPES, PH 7.0, VAPOR DIFFUSION	Resolution 1.60 Å R-free 0.226
3JTC Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins Deposited 2009-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 43–75（33 aa） Fragment：GLA domain (UNP residues 43-75)	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PTY PHOSPHATIDYLETHANOLAMINE × 1 MG MAGNESIUM ION × 2 CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；PEG 400, potassium chloride, magnesium chloride, calcium chloride, HEPES, PH 7.0, VAPOR DIFFUSION	Resolution 1.60 Å R-free 0.226
4DT7 Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C Deposited 2012-02-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 204–223（20 aa） Fragment：UNP residues 204-223	Not recorded	NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M Tris, pH 8.5, 0.2 M Na acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.218
4DT7 Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of protein C Deposited 2012-02-20	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 204–223（20 aa） Fragment：UNP residues 204-223	Not recorded	NA SODIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M Tris, pH 8.5, 0.2 M Na acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.218
6M3B hAPC-c25k23 Fab complex Deposited 2020-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 212–461（250 aa） Chain D 43–197（155 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1% n-Octyl-beta-D-glucoside, 0.1M sodium citrate tribasic dehydrate pH 5.5, 22% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.247
6M3C hAPC-h1573 Fab complex Deposited 2020-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 212–461（250 aa） Chain B 43–197（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M sodium fluoride, 20% (w/v) PEG 3350	Resolution 3.70 Å R-free 0.302
6M3C hAPC-h1573 Fab complex Deposited 2020-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 212–461（250 aa） Chain D 43–197（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M sodium fluoride, 20% (w/v) PEG 3350	Resolution 3.70 Å R-free 0.302
6M3C hAPC-h1573 Fab complex Deposited 2020-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 212–461（250 aa） Chain I 43–197（155 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M sodium fluoride, 20% (w/v) PEG 3350	Resolution 3.70 Å R-free 0.302
8JRU Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state Deposited 2023-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 205–216（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8JRV Cryo-EM structure of the glucagon receptor bound to glucagon and beta-arrestin 1 Deposited 2023-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 205–216（12 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9BVM Vitamin K-dependent gamma-carboxylase with protein C propeptide and glutamate-rich region and with vitamin K hydroquinone Deposited 2024-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 19–88（70 aa）	Not recorded	A1AVC vitamin K1 hydroquinone × 1 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9MOV Cryo-EM structure of factor Va bound to activated protein C Deposited 2024-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 43–188（146 aa） Chain D 212–451（240 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S360A	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

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PROC_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–240； UniProt 212–451

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9mot
Deposition date deposition_date	2024-12-27
Structure title title	Cryo-EM structure of factor Va bound to activated protein C
Keywords keywords	Coagulation, Activated Factor V, Activated Protein C, BLOOD CLOTTING; BLOOD CLOTTING
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.19 Å
Radius of gyration Rg (electron density) rg_electron	37.72 Å
Forward intensity I(0) i0	492409000.00
Molecular weight molecular_weight	180370.0 kDa
Excluded volume excluded_volume	225250 Å³
Envelope volume envelope_volume	288970 Å³
Hydration-shell volume shell_volume	62244 Å³
Envelope diameter envelope_diameter	127.4 Å
Shell Rg shell_rg	44.77 Å
Envelope Rg envelope_rg	37.96 Å
Shape Rg shape_rg	37.72 Å
Total Rg total_rg	38.11 Å
Total atoms total_atoms	12708
Residues n_residues	1561
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	125.5 Å
Rg (real space) rg_real	38.14 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	4.9240e+08
I(0) uncertainty (real space) i0_real_error	8.2090e+06
Rg (reciprocal space) rg_reciprocal	38.18 Å
I(0) (reciprocal space) i0_reciprocal	492400000.0000
Solution quality estimate total_estimate	0.8895
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.9 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.429
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	110000000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.924

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Coagulation factor Va heavy chain
Molecular weight formula_weight	81274.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	12708

AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGPTLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREYTYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFDKQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFSIHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKNCPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIGKHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPHGVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSDVDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCENPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTGHSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDDDEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIR

Entity 2 Entity 2 polymer

Description description	Coagulation factor Va light chain
Molecular weight formula_weight	75283.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDPRGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEWFKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQKGILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIYSLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLEMKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWEPRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEFYVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPTLRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Entity 3 Entity 3 polymer

Description description	Vitamin K-dependent protein C heavy chain
Molecular weight formula_weight	26949.8 kDa
Mutation mutation	S360A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

LIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLRRWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELNQAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGILGDRQDACEGDAGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mesocricetus auratus

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	nat
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.15 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	384239

fit	/app/data/saxs_computation/mo/9mot/9mot.fit
pddf	/app/data/pr_computation/mo/9mot/9mot.pr.out
profile	/app/data/saxs_computation/mo/9mot/9mot.dat

Cryo-EM structure of factor Va bound to activated protein C

1. Protein Identity and Related Structures Protein Identity & Related Structures

Coagulation factor Va heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Vitamin K-dependent protein C heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)