SMTL ID : 2aer.1

Crystal Structure of Benzamidine-Factor VIIa/Soluble Tissue Factor complex.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GLC.1: 3 residues within 4Å: Chain A: Q.49, S.52, Y.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.49, A:S.52, A:Y.68

1 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.2: 7 residues within 4Å: Chain A: G.58, S.60, F.71, C.72, L.73 Chain C: R.127, F.136 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.60, C:R.127, C:R.127 Hydrophobic interactions: C:F.136

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.25, R.28, E.29 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: E.16, E.26 Ligands: CA.7 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP)

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.25, E.26, E.29 No protein-ligand interaction detected (PLIP) CA.5: 3 residues within 4Å: Chain A: E.16, E.26, E.29 No protein-ligand interaction detected (PLIP) CA.7: 6 residues within 4Å: Chain A: A.1, N.2, E.7, E.16, E.20 Ligands: MG.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.1, H2O.3 CA.8: 3 residues within 4Å: Chain A: E.6, R.15, E.20 No protein-ligand interaction detected (PLIP) CA.10: 5 residues within 4Å: Chain A: D.46, G.47, Q.49, D.63, Q.64 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.46, A:G.47, A:D.63, H2O.3, H2O.20 CA.11: 5 residues within 4Å: Chain B: E.58, D.60, E.63, H.64, E.68 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, B:D.60, B:E.63, B:E.68, H2O.9, H2O.15

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 7 residues within 4Å: Chain B: Y.180, S.181, D.182, G.183, A.217, T.218, H.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.183, B:A.217 Water bridges: B:S.184, B:T.218

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 3 residues within 4Å: Chain B: H.64, E.68, S.70 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.68, H2O.10, H2O.11, H2O.11, H2O.16 ZN.14: 3 residues within 4Å: Chain B: K.9, G.57, H.105 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.57, H2O.7

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

CL.15: 4 residues within 4Å: Chain B: K.189, G.213, G.215 Ligands: BEN.17 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: R.71, R.72, H.97, Q.98 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain C: D.125, E.126, S.138, L.139, R.140, Y.149, N.169 Ligand excluded by PLIP

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.17: 13 residues within 4Å: Chain B: D.186, S.187, C.188, K.189, S.192, V.210, S.211, W.212, G.213, G.215, C.216, G.223 Ligands: CL.15 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.189, B:V.210 Hydrogen bonds: B:D.186, B:G.215 Water bridges: B:W.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bajaj, S.P. et al., High Resolution Structures of p-Aminobenzamidine- and Benzamidine-VIIa/Soluble Tissue Factor: Unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+ and Zn2+ sites in factor VIIa. J.Biol.Chem. (2006)

Release Date

2006-07-04

Peptides

Coagulation factor VII: A
Coagulation factor VII: B
Tissue factor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
T

Coagulation factor VII

Coagulation factor VII

Tissue factor

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