SMTL ID : 5wwv.1 (3 other biounits)

Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 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, I.202, Y.228, G.281, G.283, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 7V3.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.44, A:V.47, A:I.202 Hydrogen bonds: A:A.8, A:G.9, A:I.11, A:G.12, A:D.37, A:R.38, A:T.44, A:T.44, 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:G.315, A:L.316, A:T.317 FAD.8: 33 residues within 4Å: Chain B: I.6, G.7, A.8, G.9, V.10, I.11, G.12, A.36, D.37, R.38, T.43, T.44, T.45, A.48, G.50, L.51, R.162, K.163, V.164, C.181, T.182, G.183, W.185, I.202, Y.228, G.281, P.284, G.312, G.313, Y.314, G.315, L.316, T.317 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:A.48, B:I.202 Hydrogen bonds: B:A.8, B:G.9, B:I.11, B:G.12, B:D.37, B:D.37, B:R.38, B:T.43, 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

1 x 7V3: (S)-(4-chlorophenyl)-phenyl-methanamine(Non-covalent)

7V3.2: 10 residues within 4Å: Chain A: A.49, L.51, I.215, Y.224, Y.228, I.229, A.230, F.242, G.313 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.49, A:I.215, A:Y.224, A:Y.224, A:Y.224, A:Y.228, A:Y.228, A:Y.228 Hydrogen bonds: A:Y.224 pi-Stacking: A:Y.224, A:F.242 Halogen bonds: A:I.229

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: P.41, D.46, R.142, K.204, Y.279 Ligands: MPD.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.142, A:Y.279 Hydrogen bonds: A:P.41 MPD.4: 6 residues within 4Å: Chain A: P.41, F.42, V.47, Y.279, T.280 Ligands: MPD.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.42, A:V.47 Hydrogen bonds: A:T.280 MPD.5: 3 residues within 4Å: Chain A: F.39, F.159, L.161 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.39, A:F.159, A:L.161 MPD.6: 1 residues within 4Å: Chain A: L.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.161 MPD.9: 2 residues within 4Å: Chain B: R.38, F.42 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.42 Hydrogen bonds: B:R.38 MPD.10: 4 residues within 4Å: Chain B: R.142, K.143, Q.146, Q.234 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.234 Hydrogen bonds: B:K.143, B:Q.146

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

SO4.7: 4 residues within 4Å: Chain A: T.118, P.119, R.120 Chain B: L.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.118, A:R.120 Salt bridges: A:R.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yasukawa, K. et al., Tailoring D-amino acid oxidase from the pid kidney to R-stereoselective amine oxidase and its use in the deracemization of 4-chlorobenzhydrylamine. To Be Published

Release Date

2018-01-17

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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