SMTL ID : 2e82.3 (2 other biounits)

Crystal structure of human D-amino acid oxidase complexed with imino-DOPA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, L.189, I.202, Y.228, G.281, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: IM3.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:V.47, A:I.202, A:R.283 Hydrogen bonds: A:A.8, A:G.9, A:V.10, A:D.37, A:R.38, A:T.44, A:T.45, A:T.45, A:A.49, A:G.50, A:L.51, A:L.51, A:V.164, A:V.164, A:G.183, A:G.312, A:G.315, A:L.316, A:T.317 pi-Cation interactions: A:R.283 FAD.3: 37 residues within 4Å: Chain B: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, L.189, I.202, G.281, F.282, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: IM3.4 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.202, B:R.283 Hydrogen bonds: B:A.8, B:G.9, B:D.37, B:D.37, B:R.38, B:T.44, B:T.44, B:T.44, B:T.45, B:A.49, B:G.50, B:L.51, B:L.51, B:V.164, B:V.164, B:G.312, B:G.315, B:L.316, B:T.317, B:T.317 Water bridges: B:G.12 FAD.5: 35 residues within 4Å: Chain C: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, R.162, K.163, V.164, T.182, G.183, W.185, I.202, G.281, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: IM3.6 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:V.47, C:I.202, C:R.283 Hydrogen bonds: C:A.8, C:G.9, C:V.10, C:D.37, C:R.38, C:R.38, C:T.44, C:T.45, C:T.45, C:A.49, C:G.50, C:L.51, C:L.51, C:V.164, C:V.164, C:G.312, C:Y.314, C:G.315, C:L.316, C:T.317 FAD.7: 38 residues within 4Å: Chain D: I.6, G.7, A.8, G.9, V.10, I.11, A.36, D.37, R.38, T.43, T.44, T.45, V.47, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, L.189, I.202, Y.228, G.281, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: IM3.8 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:V.47, D:I.202, D:R.283 Hydrogen bonds: D:A.8, D:G.9, D:D.37, D:R.38, D:T.44, D:T.44, D:T.44, D:T.45, D:A.49, D:G.50, D:L.51, D:L.51, D:V.164, D:V.164, D:G.312, D:G.315, D:L.316, D:T.317, D:T.317 Water bridges: D:Q.53, D:G.183 pi-Cation interactions: D:R.283

4 x IM3: (2E)-3-(3,4-DIHYDROXYPHENYL)-2-IMINOPROPANOIC ACID(Non-covalent)

IM3.2: 8 residues within 4Å: Chain A: Q.53, T.216, H.217, Y.224, Y.228, R.283, G.313 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.53, A:H.217, A:Y.228, A:G.313 Salt bridges: A:R.283 pi-Stacking: A:Y.224, A:Y.228 IM3.4: 8 residues within 4Å: Chain B: Q.53, L.215, H.217, Y.224, Y.228, R.283, G.313 Ligands: FAD.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.215, B:Y.228 Hydrogen bonds: B:Q.53, B:P.54, B:G.313 Salt bridges: B:R.283 pi-Stacking: B:Y.224 IM3.6: 10 residues within 4Å: Chain C: Q.53, L.215, T.216, H.217, I.223, Y.224, Y.228, R.283, G.313 Ligands: FAD.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.215, C:Y.228 Hydrogen bonds: C:Q.53, C:H.217, C:Y.228, C:G.313 Salt bridges: C:R.283 pi-Stacking: C:Y.224 IM3.8: 9 residues within 4Å: Chain D: Q.53, L.215, T.216, H.217, Y.224, Y.228, R.283, G.313 Ligands: FAD.7 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.215 Hydrogen bonds: D:Q.53, D:H.217, D:Y.228, D:G.313 Water bridges: D:Q.53, D:P.54 Salt bridges: D:R.283 pi-Stacking: D:Y.224, D:Y.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawazoe, T. et al., Structural basis of d-DOPA oxidation by d-amino acid oxidase: Alternative pathway for dopamine biosynthesis. Biochem.Biophys.Res.Commun. (2007)

Release Date

2007-03-06

Peptides

D-amino-acid oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-amino-acid oxidase

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