SMTL ID : 6kbp.1 (1 other biounit)

Crystal structure of human D-amino acid oxidase mutant (P219L) complexed with benzoate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 36 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, Y.228, G.281, R.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: BEZ.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:V.47, A:R.283 Hydrogen bonds: A:A.8, A:G.9, A:V.10, A:I.11, 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.312, A:Y.314, A:G.315, A:L.316, A:T.317, A:T.317 Water bridges: A:G.12, A:D.37, A:V.184, A:V.184, A:Y.228, A:H.311 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, V.47, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, 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: BEZ.4, ACT.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:V.47, B:I.202, B:R.283 Hydrogen bonds: B:A.8, B:G.9, B:I.11, B:D.37, B:R.38, B:T.44, B:T.45, 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:Y.314, B:G.315, B:L.316, B:T.317 Water bridges: B:G.12, B:T.44, B:G.183, B:V.184, B:V.184 pi-Cation interactions: B:R.283

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 7 residues within 4Å: Chain A: L.215, Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.215, A:I.230 Hydrogen bonds: A:Y.228 Salt bridges: A:R.283 pi-Stacking: A:Y.224, A:Y.228 BEZ.4: 6 residues within 4Å: Chain B: Y.224, Y.228, I.230, R.283, G.313 Ligands: FAD.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.230 Hydrogen bonds: B:Y.228, B:G.313 Salt bridges: B:R.283 pi-Stacking: B:Y.224, B:Y.228

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 3 residues within 4Å: Chain B: D.37, R.38 Ligands: FAD.3 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.37 Water bridges: B:K.163, B:K.163 Salt bridges: B:R.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rachadech, W. et al., Crystal structure of human D-amino acid oxidase mutant (P219L) complexed with benzoate. To Be Published

Release Date

2020-07-08

Peptides

D-amino-acid oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-amino-acid oxidase

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