SMTL ID : 8qyw.1

Human Pyridoxine-5'-phosphate oxidase mutant R225H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: E.117, S.118, R.119, K.122, S.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.178 Salt bridges: A:K.122 PO4.3: 3 residues within 4Å: Chain A: T.250, H.251, R.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.252 Salt bridges: A:H.251, A:R.252 PO4.4: 2 residues within 4Å: Chain B: H.230 Ligands: FMN.2 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.230 PO4.5: 4 residues within 4Å: Chain A: K.103, R.164, P.165, S.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.168 Salt bridges: A:K.103, A:R.164 PO4.6: 5 residues within 4Å: Chain B: E.117, S.118, R.119, K.122, S.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.178 Salt bridges: B:K.122 PO4.8: 3 residues within 4Å: Chain B: T.250, H.251, R.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.252 Salt bridges: B:H.251, B:R.252 PO4.9: 2 residues within 4Å: Chain A: H.230 Ligands: FMN.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.230 PO4.10: 4 residues within 4Å: Chain B: K.103, R.164, P.165, S.168 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.168 Water bridges: B:Y.160, B:Y.160 Salt bridges: B:K.103, B:R.164

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: PO4.4 24 PLIP interactions: 15 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:M.99, A:L.101, B:Y.135, B:W.222, B:W.222, B:W.222 Hydrogen bonds: A:M.99, A:M.99, A:L.101, A:F.113, A:T.114, A:S.118, A:R.119, A:K.120, A:K.120, A:Q.177, A:S.178, B:Q.142, B:R.144, B:W.222 Salt bridges: A:R.98, A:K.120, B:R.144, B:R.232 FMN.7: 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: PO4.9 23 PLIP interactions: 14 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:M.99, B:L.101, A:Y.135, A:W.222, A:W.222, A:W.222 Hydrogen bonds: B:M.99, B:M.99, B:L.101, B:F.113, B:S.118, B:R.119, B:K.120, B:K.120, B:Q.177, B:S.178, A:Q.142, A:R.144, A:W.222 Salt bridges: B:R.98, B:K.120, A:R.144, A:R.232

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