SMTL ID : 9mov.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: D.136, P.137, P.138, E.249, N.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.269 NAG.2: 4 residues within 4Å: Chain A: Y.204, N.211, A.290, G.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.211, A:G.291 NAG.3: 1 residues within 4Å: Chain A: N.432 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain B: K.185, M.191, N.437, D.460 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.191, B:M.191 NAG.5: 1 residues within 4Å: Chain B: N.130 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain C: L.96, N.97, S.99 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.96 Hydrogen bonds: C:S.99 NAG.14: 2 residues within 4Å: Chain D: H.77, N.79 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.77 NAG.15: 2 residues within 4Å: Chain D: N.160, E.161 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain D: K.142, R.143, N.144 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.144

7 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain C: E.7, E.26, E.29 Ligands: CA.11 No protein-ligand interaction detected (PLIP) CA.8: 5 residues within 4Å: Chain C: A.1, E.6, E.16, E.20 Ligands: CA.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:A.1 CA.9: 2 residues within 4Å: Chain C: E.14, E.19 No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain C: E.25, E.29 No protein-ligand interaction detected (PLIP) CA.11: 6 residues within 4Å: Chain C: E.7, E.16, E.26, E.29 Ligands: CA.7, CA.13 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain C: E.20 No protein-ligand interaction detected (PLIP) CA.13: 8 residues within 4Å: Chain C: A.1, N.2, E.6, E.7, E.16, E.26 Ligands: CA.8, CA.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:A.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mohammed, B.M. et al., Cryo-EM structure of coagulation factor Va bound to activated protein C. Blood (2025)

Release Date

2025-05-21

Peptides

Coagulation factor Va heavy chain: A
Coagulation factor Va light chain: B
Vitamin K-dependent protein C: C
Vitamin K-dependent protein C heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Coagulation factor Va heavy chain

Coagulation factor Va light chain

Vitamin K-dependent protein C

Vitamin K-dependent protein C heavy chain

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