SMTL ID : 6ylz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 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, Q.146, S.147 Chain B: Q.111, W.191, R.201 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.68, A:L.70, 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, A:S.147, B:Q.111, B:W.191 Water bridges: A:R.88, B:R.201, B:R.201 Salt bridges: A:R.67, A:R.88, A:K.89, B:R.201 FMN.5: 15 residues within 4Å: Chain A: 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 23 PLIP interactions: 7 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: 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, B:S.147 Water bridges: A:R.201, A:R.201, B:R.88 Salt bridges: A:R.201, B:R.67, B:R.88, B:K.89

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

SO4.2: 2 residues within 4Å: Chain A: S.148, R.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.149 Salt bridges: A:R.149 SO4.3: 5 residues within 4Å: Chain A: R.23, R.24, R.215 Chain B: A.152, R.153 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.24, B:R.153 Water bridges: A:R.25, B:S.151, B:G.154 Salt bridges: A:R.23, A:R.215 SO4.6: 2 residues within 4Å: Chain B: S.148, R.149 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.149 Salt bridges: B:R.149 SO4.7: 5 residues within 4Å: Chain A: A.152, R.153 Chain B: R.23, R.24, R.215 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.24, A:R.153 Water bridges: B:R.25, A:S.151, A:G.154 Salt bridges: B:R.23, B:R.215

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

PO4.4: 2 residues within 4Å: Chain A: R.23, R.25 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.25, A:R.25 Salt bridges: A:R.23, A:R.25 PO4.8: 2 residues within 4Å: Chain B: R.23, R.25 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.25, B:R.25 Salt bridges: B:R.23, B:R.25

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

2021-04-14

Peptides

Pyridoxine/pyridoxamine 5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Pyridoxine/pyridoxamine 5'-phosphate oxidase

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