SMTL ID : 3th3.1

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 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

FUC.1: 5 residues within 4Å: Chain A: G.58, S.60, L.73 Chain C: R.126, F.135 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.135, A:L.73 Hydrogen bonds: C:R.126, C:R.126

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: G.47, Q.49, D.63, Q.64, Q.66, S.67 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.47, A:D.63, A:Q.64, H2O.1 CA.5: 5 residues within 4Å: Chain B: E.58, D.60, E.63, H.64, E.68 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, B:E.63, B:E.68, H2O.2, H2O.3

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

BGC.3: 4 residues within 4Å: Chain A: Q.49, S.52, P.54, Y.68 No protein-ligand interaction detected (PLIP)

1 x 0GE: N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-alpha-glutamyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]glycinamide(Covalent)

0GE.4: 15 residues within 4Å: Chain B: H.41, T.87, D.167, P.169, D.186, S.187, C.188, K.189, S.192, S.211, W.212, G.213, Q.214, G.215, G.223 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.169 Hydrogen bonds: B:S.187, B:S.192, B:S.211, B:G.213, B:G.213, B:G.215, B:G.215 Water bridges: B:W.212 Salt bridges: B:D.186

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

CL.6: 4 residues within 4Å: Chain B: R.71, R.72, H.97, Q.98 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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