SMTL ID : 1nl2.1

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM AND LYSOPHOSPHOTIDYLSERINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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: 4 residues within 4Å: Chain A: N.77, R.111, 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: 3 residues within 4Å: Chain A: N.101, S.102, T.103 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.101 Hydrogen bonds: A:N.101, A:T.103, A:T.103 Water bridges: A:S.102

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 No protein-ligand interaction detected (PLIP) CA.7: 6 residues within 4Å: Chain A: A.1, E.7, E.17, E.21 Ligands: CA.6, LPS.13 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.1, H2O.2 CA.8: 2 residues within 4Å: Chain A: E.21 Ligands: LPS.13 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain A: E.15, E.20 No protein-ligand interaction detected (PLIP)

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

CL.10: 3 residues within 4Å: Chain A: W.126, R.136, E.138 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: H.96, K.97, R.135 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: R.91, R.111, E.112 Ligand excluded by PLIP

1 x LPS: O-{HYDROXY[((2R)-2-HYDROXY-3-{[(1S)-1-HYDROXYPENTADECYL]OXY}PROPYL)OXY]PHOSPHORYL}-L-SERINE(Non-covalent)

LPS.13: 10 residues within 4Å: Chain A: K.3, F.5, L.6, E.7, R.10, R.16, E.17, E.21 Ligands: CA.7, CA.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5, A:F.5, A:L.6 Hydrogen bonds: A:L.6 Water bridges: A:A.1, A:R.16 Salt bridges: A:K.3, A:K.3, A:R.10, A:R.16

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