SMTL ID : 8qyt.1

Human Pyridoxine-5'-phosphate oxidase in complex with PLP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

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

BME.1: 4 residues within 4Å: Chain A: C.75, P.76, D.77, P.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.138 BME.5: 4 residues within 4Å: Chain B: C.75, P.76, D.77, P.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.77, B:P.138

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 17 residues within 4Å: Chain A: R.98, M.99, L.100, L.101, F.113, T.114, S.118, R.119, K.120, Q.177, S.178 Chain B: Y.135, Q.142, R.144, W.222, R.232 Ligands: PLP.3 24 PLIP interactions: 14 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:M.99, A:L.101, B:Y.135, B:W.222, B:W.222 Hydrogen bonds: A:M.99, A:M.99, A:L.101, A:F.113, A:R.119, A:K.120, A:K.120, A:Q.177, A:S.178, B:Q.142, B:W.222 Water bridges: A:R.119, B:R.144, B:R.144, B:R.144 Salt bridges: A:R.98, A:K.120, B:R.144, B:R.232 FMN.6: 17 residues within 4Å: Chain A: Y.135, Q.142, R.144, W.222, R.232 Chain B: R.98, M.99, L.100, L.101, F.113, T.114, S.118, R.119, K.120, Q.177, S.178 Ligands: PLP.7 25 PLIP interactions: 15 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:M.99, B:L.101, A:Y.135, A:W.222, A:W.222 Hydrogen bonds: B:M.99, B:M.99, B:L.101, B:F.113, B:T.114, B:R.119, B:K.120, B:K.120, B:Q.177, B:S.178, A:Q.142, A:W.222 Water bridges: B:R.119, A:R.144, A:R.144, A:R.144 Salt bridges: B:R.98, B:K.120, A:R.144, A:R.232

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

PLP.3: 9 residues within 4Å: Chain A: L.101, K.103, Y.160, R.164, Q.177 Chain B: R.228, H.230, P.264 Ligands: FMN.2 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:Y.160, A:R.164, B:H.230 Salt bridges: A:K.103, A:R.164, B:R.228 Hydrophobic interactions: B:R.228 Water bridges: B:R.228, B:R.228, B:R.228 PLP.7: 9 residues within 4Å: Chain A: R.228, H.230, P.264 Chain B: L.101, K.103, Y.160, R.164, Q.177 Ligands: FMN.6 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:Y.160, B:Y.160, B:R.164, A:H.230 Salt bridges: B:K.103, B:R.164, A:R.228 Hydrophobic interactions: A:R.228 Water bridges: A:R.228, A:R.228, A:R.228

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: E.71, Q.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.70 NA.8: 2 residues within 4Å: Chain B: E.71, Q.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barile, A. et al., Identification of the pyridoxal 5'-phosphate allosteric site in human pyridox(am)ine 5'-phosphate oxidase. Protein Sci. (2024)

Release Date

2024-02-07

Peptides

Pyridoxine-5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyridoxine-5'-phosphate oxidase