SMTL ID : 5paf.1

Crystal Structure of Factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)-methylsulfonylamino]-5-chlorophenyl]acetamide;2,2,2-trifluoroacetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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.2: 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.8: 5 residues within 4Å: Chain B: S.162, S.168, P.169, H.221, F.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.162, B:F.222, B:F.222 GOL.9: 8 residues within 4Å: Chain A: I.50, L.53 Chain B: C.7, E.11, C.12, L.128, V.147, W.204 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.11

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

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

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

SO4.5: 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 SO4.6: 5 residues within 4Å: Chain B: H.41, K.189, G.190, S.192 Ligands: 7LR.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.190, B:S.192, B:S.192 Water bridges: B:K.189, B:S.192, B:S.192 Salt bridges: B:H.41 SO4.7: 2 residues within 4Å: Chain B: S.241, E.242 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.242 Water bridges: B:R.240

1 x 7LR: N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)-methylsulfonylamino]-5-chlorophenyl]acetamide(Non-covalent)

7LR.10: 20 residues within 4Å: Chain B: H.41, D.44, K.45, G.85, 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 Ligands: SO4.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:H.41, B:V.210, B:W.212 Hydrogen bonds: B:H.41, B:K.45, B:S.187, B:S.192, B:S.192, B:G.213, B:G.215 Water bridges: B:D.44, B:G.85, B:G.85, B:W.212, B:Q.214 Salt bridges: B:D.186 pi-Stacking: B:H.41 Halogen bonds: B:S.211

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.11: 4 residues within 4Å: Chain B: N.88, H.89, T.172, Y.174 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.88

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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