SMTL ID : 3pzs.1

Crystal Structure of a pyridoxamine kinase from Yersinia pestis CO92

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: S.187, H.192, C.195, E.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.192, A:H.192, A:C.195 NA.7: 4 residues within 4Å: Chain B: S.187, H.192, C.195, E.197 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.192, B:E.197, B:E.197

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

SO4.2: 5 residues within 4Å: Chain A: V.222, G.223, V.224, G.225, D.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.223, A:G.223, A:V.224, A:G.225, A:D.226 SO4.8: 6 residues within 4Å: Chain B: H.119, V.222, G.223, V.224, G.225, D.226 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.223, B:V.224, B:G.225, B:D.226 Water bridges: B:H.119 Salt bridges: B:H.119

6 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 6 residues within 4Å: Chain A: G.17, H.18, E.265, E.267, Q.269 Chain B: W.36 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.17 BME.4: 5 residues within 4Å: Chain A: F.43, W.52, G.54, C.55, V.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.52 BME.5: 4 residues within 4Å: Chain A: R.171, C.174, T.202, A.203 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.174, A:P.178 BME.6: 5 residues within 4Å: Chain A: D.194, C.195, C.210, R.211, P.212 No protein-ligand interaction detected (PLIP) BME.9: 2 residues within 4Å: Chain B: H.51, W.52 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.52, B:W.52 BME.10: 6 residues within 4Å: Chain A: W.36 Chain B: F.16, G.17, H.18, E.267, Q.269 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.17, A:W.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brunzelle, J.S. et al., Crystal Structure of a pyridoxamine kinase from Yersinia pestis CO92. TO BE PUBLISHED

Release Date

2011-03-16

Peptides

Pyridoxamine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxamine kinase