SMTL ID : 5par.1

Crystal Structure of Factor VIIa in complex with 1H-benzimidazol-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

4 x AX7: 1H-benzimidazol-2-amine(Non-covalent)

AX7.1: 5 residues within 4Å: Chain A: P.41, T.42, V.43, E.44 Ligands: AX7.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.44 AX7.2: 3 residues within 4Å: Chain A: P.41, T.42 Ligands: AX7.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.41 AX7.10: 11 residues within 4Å: Chain B: D.186, S.187, C.188, K.189, S.192, S.211, W.212, G.213, G.215, G.223 Ligands: SO4.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.189 Hydrogen bonds: B:S.187, B:G.215 Water bridges: B:W.212, B:V.224 Salt bridges: B:D.186 AX7.11: 8 residues within 4Å: Chain B: F.43, D.44, W.49, I.78, Y.82, P.84, L.248, R.250 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.78, B:Y.82, B:P.84 Hydrogen bonds: B:F.43

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: K.49, I.50, L.53, E.54 Chain B: H.199, G.202, W.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.50, A:E.54 GOL.4: 5 residues within 4Å: Chain A: R.25, C.26, Y.30, S.31, L.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.26, A:Y.30, A:L.32, A:L.32

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain B: E.58, D.60, E.63, E.68 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, B:D.60, B:E.68, H2O.3, H2O.6

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain B: S.241, E.242 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: G.246, V.247 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 3 residues within 4Å: Chain B: M.154, T.155, R.227 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.155 Water bridges: B:R.152, B:R.227 Salt bridges: B:R.227 SO4.9: 6 residues within 4Å: Chain B: L.25, H.41, K.189, G.190, S.192 Ligands: AX7.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.190, B:S.192, B:S.192, B:S.192 Salt bridges: B:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayweg, A. et al., Crystal Structure of a Factor VIIa complex. To be published

Release Date

2017-06-21

Peptides

Coagulation factor VII light chain: A
Coagulation factor VII heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Coagulation factor VII light chain

Coagulation factor VII heavy chain

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