SMTL ID : 4ibl.1

Rubidium Sites in Blood Coagulation Factor VIIa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x BGC: beta-D-glucopyranose(Post Translational Modification)

BGC.1: 4 residues within 4Å: Chain A: Q.49, S.52, P.54, Y.68 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.53, A:Q.56, A:Y.68

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

FUC.2: 5 residues within 4Å: Chain A: G.58, S.60, F.71 Chain C: R.131, F.140 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.140 Hydrogen bonds: C:R.131

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: 2 residues within 4Å: Chain A: E.16, E.26 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.26, E.29 Ligands: RB.5 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain A: E.6, 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:D.63, A:D.63, H2O.2, H2O.16 CA.14: 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.7, H2O.8

6 x RB: RUBIDIUM ION(Non-covalent)

RB.5: 4 residues within 4Å: Chain A: E.16, E.26, E.29 Ligands: CA.4 No protein-ligand interaction detected (PLIP) RB.7: 4 residues within 4Å: Chain A: E.6, E.7, E.16, E.20 No protein-ligand interaction detected (PLIP) RB.11: 4 residues within 4Å: Chain A: E.16, E.20, Q.21, E.26 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.16, A:Q.21 RB.12: 3 residues within 4Å: Chain A: C.114, H.115, Y.118 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.118 RB.16: 4 residues within 4Å: Chain B: D.137, C.216, A.217, T.218 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.216 RB.17: 3 residues within 4Å: Chain B: S.168, P.169, N.170 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.168

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.13: 11 residues within 4Å: Chain B: D.186, S.187, K.189, S.192, V.210, S.211, W.212, G.213, G.215, C.216, G.223 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.189, B:V.210 Hydrogen bonds: B:D.186, B:S.187, B:G.215 Water bridges: B:W.212

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

CL.15: 4 residues within 4Å: Chain B: R.71, R.72, H.97, Q.98 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: E.118, R.152, R.227, S.229 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: V.20, N.21, K.47, N.48 Ligand excluded by PLIP CL.20: 7 residues within 4Å: Chain C: D.129, E.130, S.142, L.143, R.144, Y.153, N.173 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vadivel, K. et al., Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium. Acta Crystallogr.,Sect.D (2021)

Release Date

2014-04-16

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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