SMTL ID : 3th2.1

Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

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

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

FUC.2: 7 residues within 4Å: Chain A: G.58, S.60, F.71, C.72, L.73 Chain C: R.126, F.135 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.135 Hydrogen bonds: C:R.126

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.26, E.29 Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain A: E.16, E.26, E.29 Ligands: CA.4 No protein-ligand interaction detected (PLIP) CA.7: 6 residues within 4Å: Chain A: A.1, E.7, E.16, E.20 Ligands: MG.6, CA.8 No protein-ligand interaction detected (PLIP) CA.8: 4 residues within 4Å: Chain A: E.6, R.15, E.20 Ligands: CA.7 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.46, A:G.47, A:D.63, A:Q.64, H2O.5 CA.12: 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.8, H2O.11

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.11: 12 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 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

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

NA.13: 7 residues within 4Å: Chain B: Y.180, S.181, D.182, G.183, A.217, T.218, H.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.183, B:T.218 Water bridges: B:A.217

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

CL.14: 4 residues within 4Å: Chain B: R.71, R.72, H.97, Q.98 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain C: D.124, E.125, S.137, L.138, R.139, Y.148, N.168 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vadivel, K. et al., Mg2+ Is Required for Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological Ca2+. To be Published

Release Date

2012-08-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
T

Coagulation factor VII light chain

Coagulation factor VII heavy chain

Tissue factor

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