SMTL ID : 4yjh.1

Crystal structure of DAAO(Y228L/R283G) variant (R-2-phenylpyrrolidine binding form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

2 x 96B: (2R)-2-phenylpyrrolidine(Non-covalent)

96B.1: 8 residues within 4Å: Chain A: L.51, Q.53, Y.224, L.228, I.230, F.242, G.313 Ligands: FAD.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.51, A:Y.224, A:Y.224, A:L.228, A:I.230 Hydrogen bonds: A:Y.224 pi-Stacking: A:Y.224, A:F.242 96B.4: 8 residues within 4Å: Chain B: L.51, Q.53, Y.224, L.228, I.230, F.242, G.313 Ligands: FAD.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.51, B:Y.224, B:Y.224, B:L.228, B:I.230 Hydrogen bonds: B:Y.224 Water bridges: B:Y.224 pi-Stacking: B:Y.224, B:F.242

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

FAD.2: 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, G.200, I.202, G.281, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 96B.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:V.47, A:I.202 Hydrogen bonds: A:A.8, A:G.9, A:I.11, A:D.37, A:R.38, A:R.38, A:T.43, A:T.43, 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:G.183, A:H.311 FAD.5: 38 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, F.282, G.283, P.284, H.311, G.312, G.313, Y.314, G.315, L.316, T.317 Ligands: 96B.4 24 PLIP interactions: 24 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.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:Y.314, B:G.315, B:L.316, B:T.317 Water bridges: B:G.12, B:G.183

3 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.288 Salt bridges: A:R.286 SO4.6: 3 residues within 4Å: Chain B: E.21, H.24, R.155 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.25 Salt bridges: B:R.155 SO4.7: 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

Nakano, S. et al., Crystal structure of DAAO variant. To Be Published

Release Date

2016-04-06

Peptides

D-amino-acid oxidase: A
D-amino-acid oxidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-amino-acid oxidase

D-amino-acid oxidase

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