SMTL ID : 3jtc.2 (1 other biounit)

Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: H.12, Q.28, N.30, A.31, S.32 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.12 Hydrogen bonds: A:Q.28, A:N.30 NAG.2: 3 residues within 4Å: Chain A: A.90, P.92, N.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.90, A:A.90 Water bridges: A:F.91 NAG.3: 1 residues within 4Å: Chain A: N.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.155

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.4: 32 residues within 4Å: Chain A: L.11, M.13, L.14, Q.15, N.30, A.31, H.39, L.41, I.50, T.65, L.69, Y.72, Q.75, F.76, L.79, V.80, L.89, L.99, F.114, V.116, V.118, F.123, W.133, T.147, R.156, T.157, E.160, E.163, F.164, T.168, C.169, Y.172 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:M.13, A:Q.15, A:A.31, A:H.39, A:L.41, A:I.50, A:T.65, A:L.69, A:Y.72, A:Y.72, A:Y.72, A:Y.72, A:Q.75, A:F.76, A:L.79, A:V.80, A:L.89, A:L.99, A:L.99, A:F.114, A:V.116, A:V.118, A:F.123, A:W.133, A:T.147, A:F.164, A:T.168 Hydrogen bonds: A:E.163 Water bridges: A:Y.72, A:R.156, A:R.156, A:R.156 Salt bridges: A:R.156, A:R.156, A:R.156

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: E.86, R.87 Chain B: E.25, E.29 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.86, H2O.2 MG.11: 2 residues within 4Å: Chain B: E.14, E.19 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.86 Chain B: E.7, E.26, E.29 Ligands: CA.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.86, H2O.5 CA.7: 6 residues within 4Å: Chain B: E.7, E.16, E.26, E.29 Ligands: CA.6, CA.8 No protein-ligand interaction detected (PLIP) CA.8: 8 residues within 4Å: Chain B: A.1, N.2, E.6, E.7, E.16, E.26 Ligands: CA.7, CA.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.1 CA.9: 5 residues within 4Å: Chain B: A.1, E.6, E.16, E.20 Ligands: CA.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.1, H2O.6 CA.10: 1 residues within 4Å: Chain B: E.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vadivel, K. et al., Structural and Functional Studies of gamma-Carboxyglutamic Acid Domains of Factor VIIa and Activated Protein C: Role of Magnesium at Physiological Calcium. J.Mol.Biol. (2013)

Release Date

2011-04-06

Peptides

Endothelial protein C receptor: A
Vitamin K-dependent protein C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Endothelial protein C receptor

Vitamin K-dependent protein C

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