SMTL ID : 6h00.1

Crystal structure of human pyridoxine 5-phophate oxidase, R116Q variant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.100, R.161, P.162, S.165 Chain B: R.225 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.165 Salt bridges: A:K.100, A:R.161, B:R.225 SO4.2: 4 residues within 4Å: Chain A: V.170, V.171, S.172, H.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.171, A:H.173 Water bridges: A:S.176 SO4.3: 3 residues within 4Å: Chain A: T.247, H.248, R.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.249 Salt bridges: A:H.248 SO4.9: 5 residues within 4Å: Chain A: R.225 Chain B: K.100, R.161, P.162, S.165 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.165 Salt bridges: B:K.100, B:R.161, A:R.225 SO4.10: 4 residues within 4Å: Chain B: V.170, V.171, S.172, H.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.171, B:H.173 Water bridges: B:S.176 SO4.11: 3 residues within 4Å: Chain B: T.247, H.248, R.249 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.249 Salt bridges: B:H.248

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 17 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, Q.116, K.117, Q.174, S.175 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:M.96, B:L.98, A:Y.132, A:W.219, A:W.219 Hydrogen bonds: B:M.96, B:M.96, B:L.98, B:F.110, B:T.111, B:Q.116, B:K.117, B:K.117, B:Q.174, B:S.175, A:Q.139, A:W.219 Water bridges: B:F.110 Salt bridges: B:R.95, B:K.117, A:R.141, A:R.229 FMN.12: 17 residues within 4Å: Chain A: E.77, R.95, M.96, L.97, L.98, F.110, T.111, S.115, Q.116, K.117, Q.174, S.175 Chain B: Y.132, Q.139, R.141, W.219, R.229 21 PLIP interactions: 14 interactions with chain A, 7 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:Q.116, A:K.117, A:K.117, A:Q.174, A:S.175, B:Q.139, B:W.219 Water bridges: A:F.110 Salt bridges: A:R.95, A:K.117, B:R.141, B:R.229

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 8 residues within 4Å: Chain A: L.121, D.122, P.125, V.146, K.147, K.148, Y.209 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.122, A:D.122, A:K.148 EDO.6: 2 residues within 4Å: Chain A: K.148 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.148 EDO.7: 6 residues within 4Å: Chain A: H.52, L.53, T.54, Q.61, W.65, R.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.54, A:T.54, A:T.54, A:Q.61 EDO.8: 7 residues within 4Å: Chain A: E.77, A.78, A.80, Y.132, W.133 Chain B: Y.132, E.134 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.134, A:A.80, A:W.133 Water bridges: A:Y.132 EDO.13: 8 residues within 4Å: Chain B: L.121, D.122, P.125, V.146, K.147, K.148, Y.209 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.122, B:K.148 EDO.14: 2 residues within 4Å: Chain B: K.148 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.148 EDO.15: 6 residues within 4Å: Chain B: H.52, L.53, T.54, Q.61, W.65, R.138 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.54, B:T.54, B:Q.61 EDO.16: 7 residues within 4Å: Chain A: Y.132, E.134 Chain B: E.77, A.78, A.80, Y.132, W.133 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.80, B:W.133, A:E.134 Water bridges: B:Y.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mackinnon, S. et al., Crystal structure of human pyridoxine 5-phophate oxidase, R116Q variant. To Be Published

Release Date

2018-08-08

Peptides

Pyridoxine-5'-phosphate oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyridoxine-5'-phosphate oxidase