SMTL ID : 1nrg.1

Structure and Properties of Recombinant Human Pyridoxine-5'-Phosphate Oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: E.114, S.115, R.116, K.119, Q.174, S.175, S.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.114, A:E.114 Salt bridges: A:K.119 PO4.5: 7 residues within 4Å: Chain B: E.114, S.115, R.116, K.119, Q.174, S.175, S.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.114, B:E.114 Salt bridges: B:K.119

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 18 residues within 4Å: Chain A: E.77, R.95, M.96, L.97, L.98, F.110, T.111, S.115, R.116, K.117, Q.174, S.175 Chain B: Y.132, Q.139, R.141, W.219, R.229 Ligands: PLP.3 25 PLIP interactions: 15 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:M.96, A:L.98, B:Y.132, B:W.219, B:W.219 Hydrogen bonds: A:M.96, A:M.96, A:L.98, A:F.110, A:T.111, A:R.116, A:K.117, A:K.117, A:Q.174, A:S.175, B:Q.139, B:W.219 Water bridges: A:R.116, B:R.141, B:R.141, B:R.141 Salt bridges: A:R.95, A:K.117, B:R.141, B:R.229 FMN.6: 18 residues within 4Å: Chain A: Y.132, Q.139, R.141, W.219, R.229 Chain B: E.77, R.95, M.96, L.97, L.98, F.110, T.111, S.115, R.116, K.117, Q.174, S.175 Ligands: PLP.7 24 PLIP interactions: 10 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:Y.132, A:W.219, A:W.219, B:M.96, B:L.98 Hydrogen bonds: A:Q.139, A:W.219, B:M.96, B:M.96, B:L.98, B:F.110, B:R.116, B:K.117, B:K.117, B:Q.174, B:S.175 Water bridges: A:R.141, A:R.141, A:R.141, B:R.116 Salt bridges: A:R.141, A:R.229, B:R.95, B:K.117

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

PLP.3: 10 residues within 4Å: Chain A: L.98, K.100, Y.157, R.161, S.165, Q.174 Chain B: W.219, H.227, P.261 Ligands: FMN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.157, A:Y.157, A:S.165 Water bridges: A:R.161 Salt bridges: A:K.100, A:R.161 PLP.7: 10 residues within 4Å: Chain A: W.219, H.227, P.261 Chain B: L.98, K.100, Y.157, R.161, S.165, Q.174 Ligands: FMN.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.157, B:S.165 Water bridges: B:Y.157, B:Y.157, B:R.161 Salt bridges: B:K.100, B:R.161

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

BME.4: 4 residues within 4Å: Chain A: C.72, P.73, D.74, P.135 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.135 BME.8: 4 residues within 4Å: Chain B: C.72, P.73, D.74, P.135 1 PLIP interactions: 1 interactions with chain B Water bridges: B:P.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Musayev, F.N. et al., Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. Protein Sci. (2003)

Release Date

2003-02-11

Peptides

pyridoxine 5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

pyridoxine 5'-phosphate oxidase