SMTL ID : 1yxo.1

Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: H.165, H.265 Chain B: H.210 Ligands: EOH.3 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:H.265, B:H.210, EOH.3, H2O.24, H2O.44 MG.2: 4 residues within 4Å: Chain A: H.210 Chain B: H.165, H.265 Ligands: EOH.4 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:H.210, B:H.265, EOH.4, H2O.91, H2O.286

10 x EOH: ETHANOL(Non-functional Binders)

EOH.3: 7 residues within 4Å: Chain A: M.150, L.152, H.165, H.265, L.269, D.295 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.295 Water bridges: A:K.273 EOH.4: 7 residues within 4Å: Chain B: M.150, L.152, H.165, H.265, L.269, D.295 Ligands: MG.2 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.273 EOH.5: 2 residues within 4Å: Chain A: C.107, F.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.113 EOH.6: 4 residues within 4Å: Chain A: H.210, P.244, D.246, T.247 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.244 EOH.7: 4 residues within 4Å: Chain B: T.163, T.164, L.166, R.179 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.163, B:L.166 Hydrogen bonds: B:T.164, B:T.164, B:R.179 EOH.8: 6 residues within 4Å: Chain A: K.273, F.277, D.295, H.296 Chain B: D.246, T.247 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.246, A:K.273 Hydrophobic interactions: A:F.277 EOH.9: 5 residues within 4Å: Chain A: A.140, D.141, H.144, T.145, A.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.141 EOH.10: 5 residues within 4Å: Chain A: T.39, E.43, L.79, P.82, V.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.39 Hydrogen bonds: A:V.83, A:V.83 EOH.11: 4 residues within 4Å: Chain B: R.4, W.62, G.110, H.111 No protein-ligand interaction detected (PLIP) EOH.12: 7 residues within 4Å: Chain B: G.156, L.157, R.158, L.254, C.257, D.258, A.259 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.157, B:L.254 Hydrogen bonds: B:R.158, B:D.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Crystal Structure of pyridoxal phosphate biosynthetic protein PdxA PA0593. To be Published

Release Date

2005-04-05

Peptides

4-hydroxythreonine-4-phosphate dehydrogenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4-hydroxythreonine-4-phosphate dehydrogenase 1