SMTL ID : 3s9c.1

Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues 1533-1546) of human factor V

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 2 residues within 4Å: Chain A: N.227, T.229 No protein-ligand interaction detected (PLIP)

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.2: 6 residues within 4Å: Chain A: Y.19, S.24, I.26, K.52, M.55, K.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.58 Water bridges: A:K.52, A:K.52, A:K.52

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.3: 8 residues within 4Å: Chain A: R.119, C.120, R.121, N.141, I.185, C.186, N.187, G.188 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.119, A:R.119, A:R.119, A:N.187, A:G.188 Water bridges: A:E.11, A:E.11, A:R.119, A:R.121, A:N.141, A:N.141 Salt bridges: A:R.119

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 9 residues within 4Å: Chain A: K.127, S.129, T.130, C.176, H.177, E.199, P.200, C.201 Ligands: ZN.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.130 Hydrogen bonds: A:C.201 Salt bridges: A:K.127, A:H.177 ACT.5: 3 residues within 4Å: Chain A: I.128, H.138 Ligands: ZN.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.128 Salt bridges: A:H.138 ACT.6: 5 residues within 4Å: Chain A: N.10, T.102, H.103 Ligands: ACT.7, ZN.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.102 Hydrogen bonds: A:N.10 Salt bridges: A:H.103 ACT.7: 5 residues within 4Å: Chain A: I.9, N.10, H.103 Ligands: ACT.6, ZN.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.10 Salt bridges: A:H.103

3 x ZN: ZINC ION(Non-covalent)

ZN.8: 3 residues within 4Å: Chain A: H.177, E.199 Ligands: ACT.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.177, A:E.199, ACT.4 ZN.9: 2 residues within 4Å: Chain A: H.138 Ligands: ACT.5 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.138, H2O.1, H2O.6, H2O.6, ACT.5 ZN.10: 4 residues within 4Å: Chain A: N.10, H.103 Ligands: ACT.6, ACT.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.103, ACT.6, ACT.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakayama, D. et al., Structural basis of coagulation factor V recognition for cleavage by RVV-V. Febs Lett. (2011)

Release Date

2011-09-07

Peptides

Vipera russelli proteinase RVV-V gamma: A
Coagulation factor V: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Vipera russelli proteinase RVV-V gamma

Coagulation factor V

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