SMTL ID : 1nl1.1

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.77, E.112, F.114 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: R.93, N.101, S.102, T.103 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.101 Hydrogen bonds: A:R.93, A:T.103, A:T.103 Water bridges: A:P.98, A:N.101, A:N.101

7 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: E.26, E.30 No protein-ligand interaction detected (PLIP) CA.4: 4 residues within 4Å: Chain A: E.8, E.27, E.30 Ligands: CA.5 No protein-ligand interaction detected (PLIP) CA.5: 6 residues within 4Å: Chain A: E.8, E.17, E.27, E.30 Ligands: CA.4, CA.6 No protein-ligand interaction detected (PLIP) CA.6: 8 residues within 4Å: Chain A: A.1, N.2, E.7, E.8, E.17, E.27 Ligands: CA.5, CA.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.1 CA.7: 5 residues within 4Å: Chain A: A.1, E.7, E.17, E.21 Ligands: CA.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.1, H2O.6, H2O.6 CA.8: 1 residues within 4Å: Chain A: E.21 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain A: E.15, E.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, M. et al., Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins. Nat.Struct.Biol. (2003)

Release Date

2003-09-16

Peptides

Prothrombin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Prothrombin