SMTL ID : 6ymh.1

X-ray structure of the K72I, Y129F, R133L, H199A quadruple mutant of PNP-oxidase from E. coli in complex with PLP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 15 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 Chain B: E.109, Q.111, W.191, R.201, P.218 22 PLIP interactions: 9 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:W.191, B:W.191, A:I.68, A:L.70 Hydrogen bonds: B:Q.111, B:Q.111, A:I.68, A:I.68, A:L.70, A:Y.82, A:T.83, A:R.88, A:K.89, A:K.89 Water bridges: B:R.201, B:R.201, B:R.201, B:R.201 Salt bridges: B:R.201, A:R.67, A:R.88, A:K.89 FMN.3: 18 residues within 4Å: Chain A: H.106, Q.111, W.191, R.197, R.201, P.218 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 21 PLIP interactions: 6 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:H.106, A:W.191, A:W.191, B:I.68, B:L.70 Hydrogen bonds: A:Q.111, 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 Salt bridges: A:R.201, B:R.67, B:R.88, B:K.89 pi-Cation interactions: A:R.197 Water bridges: B:N.84

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

SO4.2: 6 residues within 4Å: Chain A: R.23, R.24, F.202, R.215 Chain B: A.152, R.153 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.24, B:R.153 Salt bridges: A:R.23, A:R.215

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

PLP.4: 6 residues within 4Å: Chain B: R.23, R.24, F.202, I.213, D.214, R.215 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.215 Hydrogen bonds: B:R.24, B:R.24, B:R.215 Water bridges: B:R.25 Salt bridges: B:R.23, B:R.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barile, A. et al., Identification and characterization of the pyridoxal 5'-phosphate allosteric site in Escherichia coli pyridoxine 5'-phosphate oxidase. J.Biol.Chem. (2021)

Release Date

2021-04-28

Peptides

Pyridoxine/pyridoxamine 5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Pyridoxine/pyridoxamine 5'-phosphate oxidase

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