SMTL ID : 5pb3.1

Crystal Structure of Factor VIIa in complex with 1-[[3-[4-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-5-hydroxypyrazol-1-yl]phenyl]methyl]-3-phenylurea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: C.14, S.15, D.16 Chain B: R.119 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.119 Hydrogen bonds: A:C.14, A:D.16, A:D.16 SO4.9: 3 residues within 4Å: Chain B: M.154, T.155, R.227 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.155 Water bridges: B:R.152, B:Q.156, B:R.227 Salt bridges: B:R.227

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.48, K.49, I.50, E.54 Chain B: H.199, G.202, T.203, W.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.48, A:I.50, A:I.50, A:E.54 GOL.3: 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 GOL.10: 9 residues within 4Å: Chain B: D.186, S.187, V.210, S.211, W.212, G.223, V.224, Y.225 Ligands: 9S1.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.187, B:S.211, B:W.212, B:V.224

1 x 9S1: N-({3-[4-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-5-hydroxy-1H-pyrazol-1-yl]phenyl}methyl)-N'-phenylurea(Non-covalent)

9S1.4: 18 residues within 4Å: Chain B: L.25, C.26, H.41, C.42, D.44, K.45, G.85, D.186, S.187, C.188, K.189, S.192, S.211, W.212, G.213, G.215, C.216 Ligands: GOL.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.25, B:K.189, B:K.189, B:W.212, B:W.212 Hydrogen bonds: B:H.41, B:D.44, B:D.44, B:S.192, B:S.192, B:G.213, B:G.215 Water bridges: B:S.192 pi-Stacking: B:H.41, B:W.212 pi-Cation interactions: B:K.45

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.5, H2O.8

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

CL.6: 1 residues within 4Å: Chain B: E.242 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: G.246, V.247 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.71, R.72, H.97 Ligand excluded by PLIP

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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