SMTL ID : 3hy8.1

Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W Mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 17 residues within 4Å: Chain A: R.95, M.96, L.97, L.98, F.110, T.111, S.115, R.116, K.117, Q.174 Chain B: Y.132, Q.139, R.141, W.219, W.229 Ligands: PLP.2, PO4.4 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:M.96, A:L.98, B:W.219, B:W.219, B:W.219 Hydrogen bonds: A:M.96, A:L.98, A:F.110, A:R.116, A:K.117, A:K.117, A:Q.174, B:Q.139, B:R.141 Salt bridges: A:R.95, A:K.117, B:R.141 FMN.6: 17 residues within 4Å: Chain A: Y.132, Q.139, R.141, W.219, W.229 Chain B: R.95, M.96, L.97, L.98, F.110, T.111, S.115, R.116, K.117, Q.174 Ligands: PLP.7, PO4.9 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:M.96, B:L.98, A:W.219, A:W.219, A:W.219 Hydrogen bonds: B:M.96, B:L.98, B:F.110, B:T.111, B:R.116, B:K.117, B:K.117, B:Q.174, A:Q.139, A:R.141 Salt bridges: B:R.95, B:K.117, A:R.141

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

PLP.2: 11 residues within 4Å: Chain A: E.77, L.98, K.100, Y.157, R.161, P.162, S.165 Chain B: W.219, R.225, H.227 Ligands: FMN.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.157, A:Y.157, A:S.165 Salt bridges: A:K.100, A:R.161, B:R.225 Hydrophobic interactions: B:W.219 PLP.7: 11 residues within 4Å: Chain A: W.219, R.225, H.227 Chain B: E.77, L.98, K.100, Y.157, R.161, P.162, S.165 Ligands: FMN.6 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.157, B:S.165 Salt bridges: B:K.100, B:R.161, A:R.225 Hydrophobic interactions: A:W.219

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

PO4.3: 6 residues within 4Å: Chain A: K.100, G.101, R.108, F.110, E.153, Y.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.100 Salt bridges: A:R.108 PO4.4: 7 residues within 4Å: Chain A: R.116 Chain B: R.141, E.143, E.217, W.229, R.233 Ligands: FMN.1 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.116, B:R.141 Hydrogen bonds: B:R.233 PO4.5: 3 residues within 4Å: Chain A: S.55, K.60, E.251 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.56, A:D.57, A:E.251 Salt bridges: A:K.60 PO4.8: 6 residues within 4Å: Chain B: K.100, G.101, R.108, F.110, E.153, Y.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.100, B:E.153 Salt bridges: B:R.108 PO4.9: 7 residues within 4Å: Chain A: R.141, E.143, E.217, W.229, R.233 Chain B: R.116 Ligands: FMN.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.233 Salt bridges: A:R.141, B:R.116 PO4.10: 3 residues within 4Å: Chain B: S.55, K.60, E.251 3 PLIP interactions: 3 interactions with chain B Water bridges: B:L.56, B:E.251 Salt bridges: B:K.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Musayev, F.N. et al., Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder. J.Biol.Chem. (2009)

Release Date

2009-07-28

Peptides

Pyridoxine-5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyridoxine-5'-phosphate oxidase