SMTL ID : 1g79.1

X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 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 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.24, B:R.153 Water bridges: A:R.25, B:G.154 Salt bridges: A:R.23, A:R.215 PO4.2: 2 residues within 4Å: Chain A: S.148, R.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.149 Water bridges: A:R.149 Salt bridges: A:R.149 PO4.7: 6 residues within 4Å: Chain A: A.152, R.153 Chain B: R.23, R.24, F.202, R.215 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.24, A:R.153 Water bridges: B:R.25, A:G.154 Salt bridges: B:R.23, B:R.215 PO4.8: 2 residues within 4Å: Chain B: S.148, R.149 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.149 Water bridges: B:R.149 Salt bridges: B:R.149

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 17 residues within 4Å: Chain A: D.49, R.67, I.68, V.69, L.70, Y.82, T.83, S.87, R.88, K.89, Q.146, S.147 Chain B: H.106, Q.111, W.191, R.201 Ligands: PLP.4 24 PLIP interactions: 8 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:Q.111, B:W.191, B:W.191, A:I.68, A:L.70 Hydrogen bonds: B:Q.111, B:W.191, 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 Water bridges: B:R.201, B:P.218, A:R.88 Salt bridges: B:R.201, A:R.67, A:R.88, A:K.89 FMN.9: 17 residues within 4Å: Chain A: H.106, Q.111, W.191, R.201 Chain B: D.49, R.67, I.68, V.69, L.70, Y.82, T.83, S.87, R.88, K.89, Q.146, S.147 Ligands: PLP.10 22 PLIP interactions: 7 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:Q.111, A:W.191, A:W.191, B:I.68, B:L.70 Hydrogen bonds: A:Q.111, A:W.191, 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 Water bridges: A:R.201, B:R.88 Salt bridges: A:R.201, B:R.67, B:R.88, B:K.89

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

PLP.4: 9 residues within 4Å: Chain A: L.70, K.72, Y.129, R.133, Q.146 Chain B: R.197, H.199, P.218 Ligands: FMN.3 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.129, A:Y.129, B:H.199 Water bridges: A:R.133, A:S.137, A:Q.146 Salt bridges: A:K.72, A:R.133, B:R.197 Hydrophobic interactions: B:R.197 PLP.5: 3 residues within 4Å: Chain A: K.159, S.176, F.177 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.177 Water bridges: A:K.159 Salt bridges: A:K.159 pi-Stacking: A:F.177 PLP.10: 9 residues within 4Å: Chain A: R.197, H.199, P.218 Chain B: L.70, K.72, Y.129, R.133, Q.146 Ligands: FMN.9 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.129, A:H.199 Water bridges: B:R.133, B:S.137, B:Q.146 Salt bridges: B:K.72, B:R.133, A:R.197 Hydrophobic interactions: A:R.197 PLP.11: 3 residues within 4Å: Chain B: K.159, S.176, F.177 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.177 Water bridges: B:K.159 Salt bridges: B:K.159 pi-Stacking: B:F.177

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

BME.6: 3 residues within 4Å: Chain A: C.43, P.50, T.51 No protein-ligand interaction detected (PLIP) BME.12: 3 residues within 4Å: Chain B: C.43, P.50, T.51 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safo, M.K. et al., X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution. J.Mol.Biol. (2001)

Release Date

2000-11-29

Peptides

PYRIDOXINE 5'-PHOSPHATE OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PYRIDOXINE 5'-PHOSPHATE OXIDASE

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