SMTL ID : 1ygc.2 (1 other biounit)

Short Factor VIIa with a small molecule inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.58, D.60, E.63, E.68 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.58, A:D.60, A:E.63, A:E.68, H2O.2, H2O.4 CA.2: 3 residues within 4Å: Chain A: V.101 Chain C: V.101 Ligands: CA.12 No protein-ligand interaction detected (PLIP) CA.11: 4 residues within 4Å: Chain C: E.58, D.60, E.63, E.68 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.58, C:D.60, C:E.63, C:E.68, H2O.12, H2O.14 CA.12: 3 residues within 4Å: Chain A: V.101 Chain C: V.101 Ligands: CA.2 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: M.154, T.155, R.227 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.155, A:T.155 Water bridges: A:R.152, A:Q.156, A:R.227, A:R.227 Salt bridges: A:R.227 SO4.4: 2 residues within 4Å: Chain A: S.241, E.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.242 SO4.5: 5 residues within 4Å: Chain A: S.70, R.71, R.72, H.97, Q.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.72, A:H.97, A:Q.98, A:Q.98 Salt bridges: A:H.97 SO4.6: 3 residues within 4Å: Chain A: T.86, T.87, P.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.85, A:T.87 Water bridges: A:N.88, A:N.170 SO4.7: 5 residues within 4Å: Chain A: S.162, Q.214, H.221, F.222, V.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.162, A:Q.214, A:F.222 Salt bridges: A:H.221 SO4.8: 5 residues within 4Å: Chain A: D.67, T.103, D.104, H.105 Chain B: Y.44 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.104, A:H.105, B:Y.44 Water bridges: A:D.67 Salt bridges: A:H.105 SO4.10: 4 residues within 4Å: Chain A: R.119 Chain B: C.13, S.14, D.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.15 Water bridges: B:S.14, A:R.119 Salt bridges: A:R.119 SO4.13: 3 residues within 4Å: Chain C: M.154, T.155, R.227 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.155 Water bridges: C:R.152, C:R.152, C:T.155, C:Q.156 Salt bridges: C:R.227 SO4.14: 2 residues within 4Å: Chain C: S.241, E.242 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.242 SO4.15: 5 residues within 4Å: Chain C: S.70, R.71, R.72, H.97, Q.98 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.72, C:H.97, C:Q.98, C:Q.98 Salt bridges: C:H.97 SO4.16: 3 residues within 4Å: Chain C: T.86, T.87, P.169 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.85, C:T.87 Water bridges: C:T.87, C:N.88, C:N.170 SO4.17: 5 residues within 4Å: Chain C: S.162, Q.214, H.221, F.222, V.224 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.162, C:Q.214, C:F.222 Salt bridges: C:H.221 SO4.18: 5 residues within 4Å: Chain C: D.67, T.103, D.104, H.105 Chain D: Y.44 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.104, C:H.105 Water bridges: C:T.103, C:T.103 Salt bridges: C:H.105 SO4.20: 4 residues within 4Å: Chain C: R.119 Chain D: C.13, S.14, D.15 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.15, D:D.15 Water bridges: D:S.14, C:R.119 Salt bridges: C:R.119

2 x 905: (R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5-DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY-BENZAMIDINE(Non-covalent)

905.9: 18 residues within 4Å: Chain A: H.41, D.44, K.45, T.86, T.87, D.90, D.186, S.187, C.188, K.189, S.192, V.210, S.211, W.212, G.213, G.215, C.216, G.223 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.189, A:V.210 Hydrogen bonds: A:D.186, A:S.187, A:S.187, A:S.192, A:S.192, A:G.213, A:G.215 Water bridges: A:D.44, A:W.212, A:A.217 pi-Cation interactions: A:H.41 905.19: 18 residues within 4Å: Chain C: H.41, D.44, K.45, T.86, T.87, D.90, D.186, S.187, C.188, K.189, S.192, V.210, S.211, W.212, G.213, G.215, C.216, G.223 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:K.189, C:V.210 Hydrogen bonds: C:D.186, C:S.187, C:S.187, C:S.192, C:S.192, C:G.213, C:G.215 Water bridges: C:D.44, C:W.212, C:T.218 pi-Cation interactions: C:H.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olivero, A.G. et al., A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo. J.Biol.Chem. (2005)

Release Date

2005-01-18

Peptides

Coagulation factor VII: AC
Coagulation factor VII: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
H

B
L

D
L

Coagulation factor VII

Coagulation factor VII

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