SMTL ID : 5pab.1

Crystal Structure of Factor VIIa in complex with 1-[[3-[2-hydroxy-3-(1H-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenylurea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 7XD: 1-[[3-[2-oxidanyl-3-(1~{H}-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenyl-urea(Non-covalent)

7XD.1: 17 residues within 4Å: Chain A: L.25, C.26, H.41, C.42, D.44, K.45, G.85, S.187, C.188, K.189, S.192, V.210, S.211, W.212, G.213, G.215 Ligands: GOL.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.25, A:K.189, A:K.189, A:K.189, A:V.210, A:W.212 Hydrogen bonds: A:H.41, A:D.44, A:D.44, A:S.192, A:S.192, A:S.192 Water bridges: A:G.190, A:V.224 pi-Stacking: A:H.41, A:W.212 pi-Cation interactions: A:K.45

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

CL.2: 3 residues within 4Å: Chain A: R.71, R.72, H.97 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.240 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: S.241, E.242 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: F.43, D.44, I.46, W.49, I.78, P.84, L.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.46 GOL.4: 5 residues within 4Å: Chain A: Q.24, L.25, K.189, G.190 Ligands: 7XD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.24, A:G.190 Water bridges: A:Q.24 GOL.5: 2 residues within 4Å: Chain A: H.199, W.204 No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain B: R.25, C.26, S.31, L.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.26, B:C.26, B:L.32

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: E.58, D.60, E.63, E.68 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.58, A:E.63, A:E.68, H2O.2, H2O.7

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

SO4.9: 3 residues within 4Å: Chain A: M.154, T.155, R.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.155, A:T.155 Water bridges: A:R.227, A:R.227 Salt bridges: A:R.227 SO4.11: 4 residues within 4Å: Chain A: R.119 Chain B: C.14, S.15, D.16 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:T.115, A:R.119 Salt bridges: A:R.119 Hydrogen bonds: B:C.14, B:D.16

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 heavy chain: A
Coagulation factor VII light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Coagulation factor VII heavy chain

Coagulation factor VII light chain

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