SMTL ID : 3th4.1

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 1.80 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 No protein-ligand interaction detected (PLIP)

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 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.135 Hydrogen bonds: C:R.126, C:R.126

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.25, E.29 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: E.14, E.19 No protein-ligand interaction detected (PLIP)

7 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.7, E.26, E.29 Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.5: 6 residues within 4Å: Chain A: E.7, E.16, E.26, E.29 Ligands: CA.4, CA.6 No protein-ligand interaction detected (PLIP) CA.6: 8 residues within 4Å: Chain A: A.1, N.2, E.6, E.7, E.16, E.26 Ligands: CA.5, CA.7 No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain A: A.1, E.6, E.16, E.20 Ligands: CA.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.1, H2O.2 CA.8: 1 residues within 4Å: Chain A: 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:G.47, A:D.63, H2O.1, H2O.3 CA.13: 4 residues within 4Å: Chain B: E.58, D.60, E.63, E.68 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.58, B:D.60, B:E.63, B:E.68, H2O.5

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.11: 19 residues within 4Å: Chain B: H.41, T.87, D.167, P.169, D.186, S.187, C.188, K.189, G.190, D.191, S.192, S.211, W.212, G.213, Q.214, G.215, C.216, G.223 Ligands: CL.15 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.169 Hydrogen bonds: B:S.187, B:G.190, B:S.192, B:S.211, B:G.213, B:G.213, B:G.215, B:G.215 Water bridges: B:W.212, B:A.217 Salt bridges: B:D.186

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

CL.12: 7 residues within 4Å: Chain C: D.124, E.125, S.137, L.138, R.139, Y.148, N.168 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: G.213, G.215 Ligands: 0GE.11 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: R.71, R.72, H.97 Ligand excluded by PLIP

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

NA.14: 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:A.217 Water bridges: B:A.217

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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