SMTL ID : 3wgt.1

Crystal structure of D-amino acid oxidase mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 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, A.48, A.49, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, G.200, I.202, G.281, G.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: QSC.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.202 Hydrogen bonds: A:A.8, A:G.9, 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 Water bridges: A:G.12, A:Q.53, A:G.183, A:V.184, A:V.184 FAD.5: 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, G.200, I.202, G.281, G.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: QSC.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:V.47, B:I.202 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:G.315, B:L.316, B:T.317 Water bridges: B:G.12, B:T.44, B:Q.53, B:G.183, B:V.184, B:V.184, B:H.311, B:T.317

2 x QSC: (1R)-1-phenylethanamine(Non-covalent)

QSC.2: 6 residues within 4Å: Chain A: Y.224, L.228, I.230, F.242, G.313 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.224, A:Y.224, A:L.228, A:I.230 Hydrogen bonds: A:G.313 pi-Stacking: A:Y.224, A:F.242 QSC.6: 6 residues within 4Å: Chain B: Y.224, L.228, I.230, F.242, G.313 Ligands: FAD.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.224, B:L.228, B:I.230 Hydrogen bonds: B:G.313 Water bridges: B:Y.224 pi-Stacking: B:Y.224, B:F.242

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

SO4.3: 5 residues within 4Å: Chain A: R.286, Q.288, V.289, R.290, E.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.288 Water bridges: A:R.286 Salt bridges: A:R.286 SO4.4: 3 residues within 4Å: Chain A: T.118, P.119, R.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.120 Salt bridges: A:R.120 SO4.7: 2 residues within 4Å: Chain B: H.24, R.155 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.25 Salt bridges: B:R.155 SO4.8: 2 residues within 4Å: Chain B: R.142, Q.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.146 Salt bridges: B:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yasukawa, K. et al., Tailoring D-amino acid oxidase from the pig kidney to R-stereoselective amine oxidase and its use in the deracemization of alpha-methylbenzylamine. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-04-02

Peptides

D-amino-acid oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-amino-acid oxidase