SMTL ID : 5pai.1

human factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-1-[3-[[(3,5-dimethyl-1,2-oxazol-4-yl)carbamoylamino]methyl]phenyl]-5-hydroxypyrazole-4-carboxamide at 1.73A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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.2: 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.7, H2O.11

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

CL.3: 3 residues within 4Å: Chain B: R.50, G.246, V.247 Ligand excluded by PLIP

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

SO4.4: 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 SO4.5: 3 residues within 4Å: Chain B: S.241, E.242, R.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.242, B:R.244 Water bridges: B:R.240, B:R.244

1 x 7YM: N-(2-amino-1H-benzimidazol-5-yl)-1-[3-[[(3,5-dimethyl-1,2-oxazol-4-yl)carbamoylamino]methyl]phenyl]-5-hydroxypyrazole-4-carboxamide(Non-covalent)

7YM.6: 20 residues within 4Å: Chain B: L.25, C.26, H.41, C.42, D.44, K.45, P.84, G.85, D.186, S.187, C.188, K.189, S.192, V.210, S.211, W.212, G.213, G.215, C.216, G.223 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:D.44, B:K.189, B:V.210, B:W.212, B:W.212, B:W.212 Hydrogen bonds: B:H.41, B:H.41, B:D.44, B:D.44, B:S.192, B:S.192, B:G.215, B:G.215 Water bridges: B:K.189, B:K.189, B:S.192, B:A.217, B:V.224, B:V.224, B:V.224 Salt bridges: B:D.186 pi-Stacking: B:H.41, B:W.212

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
B

Coagulation factor VII light chain

Coagulation factor VII heavy chain

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