SMTL ID : 1jnw.1

Active Site Structure of E. coli pyridoxine 5'-phosphate Oxidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: R.23, R.24, F.202, R.215 Chain B: A.152, R.153 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.24, B:R.153 Water bridges: A:R.23, A:R.23, A:R.25, B:S.151, B:G.154 Salt bridges: A:R.23, A:R.215 PO4.4: 6 residues within 4Å: Chain A: A.152, R.153 Chain B: R.23, R.24, F.202, R.215 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.153, B:R.24 Water bridges: A:S.151, A:G.154, B:R.23, B:R.23, B:R.25 Salt bridges: B:R.23, B:R.215

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: Y.17, H.106, Q.111, W.191, R.201, P.218 Chain B: R.67, I.68, V.69, L.70, Y.82, T.83, S.87, R.88, K.89, Q.146, S.147 Ligands: PLP.3 23 PLIP interactions: 15 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.68, B:I.68, B:L.70, A:Q.111, A:W.191, A:W.191, A:W.191 Hydrogen bonds: B:I.68, B:I.68, B:L.70, B:Y.82, B:R.88, B:K.89, B:K.89, B:Q.146, B:S.147, A:Q.111 Salt bridges: B:R.67, B:R.88, B:K.89, A:R.201 Water bridges: A:R.201, A:R.201 FMN.5: 18 residues within 4Å: Chain A: R.67, I.68, V.69, L.70, Y.82, T.83, S.87, R.88, K.89, Q.146, S.147 Chain B: Y.17, H.106, Q.111, W.191, R.201, P.218 Ligands: PLP.6 24 PLIP interactions: 16 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:I.68, A:I.68, A:L.70, B:Q.111, B:W.191, B:W.191, B:W.191 Hydrogen bonds: A:I.68, A:I.68, A:L.70, A:Y.82, A:T.83, A:R.88, A:K.89, A:K.89, A:Q.146, A:S.147, B:Q.111 Salt bridges: A:R.67, A:R.88, A:K.89, B:R.201 Water bridges: B:R.201, B:R.201

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.3: 10 residues within 4Å: Chain A: R.14, Y.17, R.197, H.199, P.218 Chain B: K.72, Y.129, R.133, Q.146 Ligands: FMN.2 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.129, A:H.199 Water bridges: B:S.137, A:R.197 Salt bridges: B:K.72, B:R.133, A:R.14, A:R.197 PLP.6: 10 residues within 4Å: Chain A: K.72, Y.129, R.133, Q.146 Chain B: R.14, Y.17, R.197, H.199, P.218 Ligands: FMN.5 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.17, B:H.199, A:Y.129, A:Y.129 Water bridges: B:R.197, A:S.137 Salt bridges: B:R.14, B:R.197, A:K.72, A:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

di Salvo, M.L. et al., Active site structure and stereospecificity of Escherichia coli pyridoxine-5'-phosphate oxidase. J.Mol.Biol. (2002)

Release Date

2001-08-01

Peptides

Pyridoxine 5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyridoxine 5'-phosphate oxidase

Related Entries With Identical Sequence