SMTL ID : 8hy5.1

Structure of D-amino acid oxidase mutant R38H

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: 37 residues within 4Å: Chain A: I.29, G.30, A.31, G.32, V.33, I.34, A.59, D.60, H.61, T.66, T.67, T.68, A.71, A.72, G.73, L.74, R.185, K.186, V.187, C.204, T.205, G.206, W.208, I.225, G.304, F.305, R.306, P.307, H.334, G.335, G.336, Y.337, G.338, L.339, T.340 Ligands: BEZ.2, EDO.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.225, A:R.306 Hydrogen bonds: A:A.31, A:G.32, A:I.34, A:D.60, A:H.61, A:T.66, A:T.67, A:T.67, A:T.67, A:T.68, A:T.68, A:A.72, A:G.73, A:L.74, A:L.74, A:V.187, A:V.187, A:G.335, A:Y.337, A:G.338, A:L.339, A:T.340 Water bridges: A:T.67, A:G.206, A:V.207, A:V.207 FAD.4: 36 residues within 4Å: Chain B: I.29, G.30, A.31, G.32, V.33, I.34, A.59, D.60, H.61, T.66, T.67, T.68, V.70, A.71, G.73, L.74, R.185, K.186, V.187, C.204, T.205, G.206, W.208, I.225, Y.251, G.304, R.306, P.307, H.334, G.335, G.336, Y.337, G.338, L.339, T.340 Ligands: BEZ.5 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:V.70, B:I.225, B:R.306 Hydrogen bonds: B:A.31, B:G.32, B:I.34, B:D.60, B:H.61, B:T.67, B:T.67, B:T.68, B:T.68, B:A.72, B:G.73, B:L.74, B:L.74, B:V.187, B:V.187, B:G.335, B:Y.337, B:G.338, B:L.339, B:T.340, B:T.340 Water bridges: B:G.35, B:D.60, B:D.60, B:T.67, B:V.207

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 9 residues within 4Å: Chain A: L.74, Q.76, L.238, Y.247, Y.251, I.253, R.306, G.336 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.74, A:L.238, A:I.253 Hydrogen bonds: A:G.336 Salt bridges: A:R.306 pi-Stacking: A:Y.247, A:Y.251 BEZ.5: 6 residues within 4Å: Chain B: Y.247, Y.251, I.253, R.306, G.336 Ligands: FAD.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.247, B:I.253 Hydrogen bonds: B:Y.251, B:Y.251 Salt bridges: B:R.306 pi-Stacking: B:Y.251

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

EDO.3: 5 residues within 4Å: Chain A: D.60, H.61, K.186, W.208 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.61, A:K.186, A:K.186

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain B: L.145, F.148, P.149, Y.151 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khan, S. et al., Structural and mechanistic insights into ALS patient derived mutations in D-amino acid oxidase. Int.J.Biol.Macromol. (2023)

Release Date

2023-01-25

Peptides

D-amino-acid oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-amino-acid oxidase