SMTL ID : 4ha6.2 (1 other biounit)

Crystal structure of pyridoxine 4-oxidase - pyridoxamine complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 39 residues within 4Å: Chain A: V.7, G.8, G.9, G.10, S.11, A.12, I.31, E.32, A.33, W.58, A.76, R.77, G.78, R.79, L.80, G.83, S.84, S.85, L.87, H.88, A.89, M.90, G.91, S.216, R.217, V.218, C.250, A.251, G.252, E.255, R.262, H.445, D.477, A.478, P.488, I.489, H.490, V.493 Ligands: PXM.9 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:H.445 Hydrogen bonds: A:G.9, A:S.11, A:S.11, A:A.12, A:A.33, A:R.77, A:G.78, A:L.80, A:S.84, A:S.84, A:H.88, A:A.89, A:G.91, A:G.91, A:V.218, A:V.218, A:R.262, A:A.478, A:I.489, A:H.490 Water bridges: A:G.10, A:G.13, A:S.84, A:A.253, A:A.491 pi-Stacking: A:H.88, A:H.88 FAD.10: 39 residues within 4Å: Chain B: V.7, G.8, G.9, G.10, S.11, A.12, I.31, E.32, A.33, W.58, A.76, R.77, G.78, R.79, L.80, G.83, S.84, S.85, L.87, H.88, A.89, M.90, G.91, S.216, R.217, V.218, C.250, A.251, G.252, E.255, R.262, H.445, D.477, A.478, P.488, I.489, H.490, V.493 Ligands: PXM.18 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:H.445 Hydrogen bonds: B:G.9, B:S.11, B:S.11, B:A.12, B:A.33, B:R.77, B:G.78, B:L.80, B:S.84, B:S.84, B:H.88, B:A.89, B:G.91, B:G.91, B:V.218, B:V.218, B:E.255, B:R.262, B:A.478, B:I.489, B:H.490 Water bridges: B:G.10, B:G.13, B:S.84, B:A.253, B:H.490, B:A.491 pi-Stacking: B:H.88, B:H.88

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: H.144, I.187, R.188, D.189, G.190 Chain B: R.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.144, A:D.189, A:G.190 Water bridges: A:R.188 GOL.3: 9 residues within 4Å: Chain A: Y.60, E.255, A.258, R.262, I.373, E.377, L.378, D.380, L.382 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.262 Water bridges: A:L.259, A:G.375, A:D.380, A:D.380, A:L.382 GOL.4: 5 residues within 4Å: Chain A: P.267, D.269, V.270, P.283, R.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.269, A:P.283 GOL.5: 8 residues within 4Å: Chain A: M.320, R.321, A.322, D.323, S.324, F.325, R.400, A.404 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:S.324 Water bridges: A:R.400 GOL.6: 6 residues within 4Å: Chain A: T.366, S.367, R.368, A.387, Q.390, T.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.368 GOL.7: 3 residues within 4Å: Chain A: H.410, R.411, D.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.412, A:D.412 Water bridges: A:R.411 GOL.8: 2 residues within 4Å: Chain A: R.168, E.176 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain B: H.144, I.187, R.188, D.189, G.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.144, B:D.189, B:G.190 Water bridges: B:R.188 GOL.12: 9 residues within 4Å: Chain B: Y.60, E.255, A.258, R.262, I.373, E.377, L.378, D.380, L.382 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.262 Water bridges: B:L.259, B:G.375, B:D.380, B:D.380, B:L.382 GOL.13: 5 residues within 4Å: Chain B: P.267, D.269, V.270, P.283, R.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.269, B:P.283 GOL.14: 8 residues within 4Å: Chain B: M.320, R.321, A.322, D.323, S.324, F.325, R.400, A.404 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.321, B:S.324 Water bridges: B:R.400 GOL.15: 6 residues within 4Å: Chain B: T.366, S.367, R.368, A.387, Q.390, T.391 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.368 GOL.16: 3 residues within 4Å: Chain B: H.410, R.411, D.412 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.412, B:D.412 Water bridges: B:R.411 GOL.17: 2 residues within 4Å: Chain B: R.168, E.176 No protein-ligand interaction detected (PLIP)

2 x PXM: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL(Non-covalent)

PXM.9: 8 residues within 4Å: Chain A: W.48, A.89, S.314, H.444, H.445, H.446, P.488 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.48, A:A.89 Hydrogen bonds: A:S.314, A:H.444, A:H.445 pi-Stacking: A:W.48, A:H.444 PXM.18: 8 residues within 4Å: Chain B: W.48, A.89, S.314, H.444, H.445, H.446, P.488 Ligands: FAD.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.48, B:A.89 Hydrogen bonds: B:S.314, B:H.444, B:H.444, B:H.445 pi-Stacking: B:W.48, B:H.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mugo, A.N. et al., Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti. Biochim.Biophys.Acta (2013)

Release Date

2013-06-05

Peptides

Pyridoxine 4-oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyridoxine 4-oxidase

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