SMTL ID : 5edm.1

Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I )

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 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: R.92, N.100, T.102 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.359 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.29, E.32 4 PLIP interactions: 3 Ligand-Water interactions, 1 interactions with chain A Metal complexes: H2O.1, H2O.3, H2O.4, A:E.29 MG.4: 2 residues within 4Å: Chain A: E.25, E.29 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: E.26, E.29 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: E.16, E.26 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: E.20 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: E.14, E.19, R.54 No protein-ligand interaction detected (PLIP)

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

NAG.9: 1 residues within 4Å: Chain A: N.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.78 Water bridges: A:N.112, A:N.112

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain A: S.33, S.34, T.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.34, A:T.35, A:T.35 SO4.11: 4 residues within 4Å: Chain A: R.90, L.109, Q.110, E.111 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.111, A:E.111 Water bridges: A:S.101, A:S.101, A:L.109, A:E.111 Salt bridges: A:R.90 SO4.12: 2 residues within 4Å: Chain A: R.90, E.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.111 Salt bridges: A:R.90 SO4.13: 4 residues within 4Å: Chain A: T.121, M.122, G.123, T.149 No protein-ligand interaction detected (PLIP) SO4.14: 3 residues within 4Å: Chain A: S.182, A.183, Q.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.183 SO4.15: 6 residues within 4Å: Chain A: E.286, S.289, E.291, E.295, K.518, N.523 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.289, A:N.523, A:N.523 Water bridges: A:K.518 Salt bridges: A:K.518 SO4.16: 5 residues within 4Å: Chain A: E.98, I.99, Y.127, R.134, R.135 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.98, A:E.98, A:E.98, A:Y.127 Salt bridges: A:R.134, A:R.135 SO4.17: 5 residues within 4Å: Chain A: R.376, E.378, R.379, N.380, I.381 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.380, A:N.380, A:I.381 Water bridges: A:R.376, A:R.379 Salt bridges: A:R.376 SO4.19: 2 residues within 4Å: Chain A: K.288, D.419 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.288

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 8 residues within 4Å: Chain A: S.482, T.483, I.485, G.534, E.535, K.542, Y.543, F.545 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.482, A:E.535, A:E.535, A:E.535, A:Y.543

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pozzi, N. et al., How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J.Biol.Chem. (2016)

Release Date

2016-01-20

Peptides

Prothrombin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Prothrombin