SMTL ID : 8qod.1

CRYSTAL STRUCTURE OF FVIIA IN COMPLEX WITH A BENZAMIDINE-BASED INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.44, G.45, D.61, Q.62 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.44, A:G.45, A:D.61, A:D.61, H2O.37 CA.5: 2 residues within 4Å: Chain A: E.23, E.27 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: E.12, E.17 No protein-ligand interaction detected (PLIP) CA.8: 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.12, H2O.19

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.14, E.24 No protein-ligand interaction detected (PLIP)

1 x GLC: alpha-D-glucopyranose(Post Translational Modification)

GLC.3: 4 residues within 4Å: Chain A: Q.47, S.50, P.52, Y.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.47, A:Q.47 Water bridges: A:Y.66

1 x FUC: alpha-L-fucopyranose(Post Translational Modification)

FUC.4: 6 residues within 4Å: Chain A: G.56, S.58, F.69, C.70, L.71 Chain C: F.172 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.71, C:F.172 Water bridges: A:S.58

1 x WIZ: 3-[2-bromanyl-4-[(1~{S})-1-[[3-[(4-carbamimidoylphenyl)amino]-3-oxidanylidene-propanoyl]amino]ethyl]phenoxy]benzoic acid(Non-covalent)

WIZ.7: 18 residues within 4Å: Chain B: H.41, G.85, T.86, T.87, D.90, P.169, D.186, S.187, C.188, K.189, S.192, V.210, S.211, W.212, G.213, G.215, C.216, G.223 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:H.41, B:T.87, B:P.169, B:K.189, B:V.210, B:W.212 Hydrogen bonds: B:T.87, B:T.87, B:D.186, B:S.192, B:S.211, B:G.215 Water bridges: B:T.87, B:T.87, B:N.88, B:W.212, B:Q.214, B:A.217

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

CL.9: 4 residues within 4Å: Chain B: R.71, R.72, H.97, Q.98 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain C: D.161, E.162, S.174, L.175, R.176, Y.185, N.205 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tesmer, L. et al., Crystallography and molecular simulations capture S1 pocketcollapse in allosteric regulation of factor VIIa and other serine proteases. To be published

Release Date

2024-10-09

Peptides

Factor VII light chain: A
Coagulation factor VII: B
Tissue factor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Factor VII light chain

Coagulation factor VII

Tissue factor

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