SMTL ID : 7ct4.1

Crystal structure of D-amino acid oxidase from Rasamsonia emersonii strain YA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: L.29, G.30, A.31, G.32, V.33, S.34, A.54, K.55, H.56, E.64, Y.65, C.66, S.67, W.69, A.70, G.71, A.72, N.73, A.192, V.193, F.194, C.216, T.217, G.218, S.220, L.224, G.237, I.239, G.326, L.327, R.328, H.353, G.354, G.355, Y.356, G.357, Y.358, Q.359 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.239, A:R.328 Hydrogen bonds: A:A.31, A:G.32, A:V.33, A:S.34, A:S.34, A:S.34, A:K.55, A:H.56, A:H.56, A:E.64, A:C.66, A:S.67, A:S.67, A:G.71, A:N.73, A:N.73, A:N.73, A:F.194, A:F.194, A:S.220, A:G.354, A:G.357, A:Y.358, A:Q.359 Water bridges: A:G.35 pi-Cation interactions: A:R.328 FAD.2: 38 residues within 4Å: Chain B: L.29, G.30, A.31, G.32, V.33, S.34, A.54, K.55, H.56, E.64, Y.65, C.66, S.67, W.69, A.70, G.71, A.72, N.73, A.192, V.193, F.194, C.216, T.217, G.218, S.220, L.224, G.237, I.239, Y.264, G.326, R.328, H.353, G.354, G.355, Y.356, G.357, Y.358, Q.359 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:I.239, B:R.328 Hydrogen bonds: B:A.31, B:G.32, B:S.34, B:S.34, B:S.34, B:G.35, B:K.55, B:H.56, B:H.56, B:E.64, B:C.66, B:S.67, B:S.67, B:G.71, B:N.73, B:N.73, B:N.73, B:F.194, B:F.194, B:S.220, B:G.354, B:Y.356, B:G.357, B:Y.358, B:Q.359 Water bridges: B:R.328 pi-Stacking: B:Y.358 pi-Cation interactions: B:R.328 FAD.3: 39 residues within 4Å: Chain C: L.29, G.30, A.31, G.32, V.33, S.34, A.54, K.55, H.56, E.64, Y.65, C.66, S.67, W.69, A.70, G.71, A.72, N.73, A.192, V.193, F.194, C.216, T.217, G.218, S.220, L.224, G.237, Y.264, M.266, G.326, L.327, R.328, H.353, G.354, G.355, Y.356, G.357, Y.358, Q.359 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:R.328 Hydrogen bonds: C:A.31, C:G.32, C:V.33, C:S.34, C:S.34, C:S.34, C:G.35, C:K.55, C:H.56, C:H.56, C:E.64, C:C.66, C:S.67, C:S.67, C:G.71, C:N.73, C:N.73, C:N.73, C:F.194, C:F.194, C:S.220, C:G.354, C:G.357, C:Y.358, C:Q.359 Water bridges: C:L.75, C:L.219 pi-Cation interactions: C:R.328 FAD.4: 38 residues within 4Å: Chain D: L.29, G.30, A.31, G.32, V.33, S.34, A.54, K.55, H.56, E.64, Y.65, C.66, S.67, W.69, A.70, G.71, A.72, N.73, A.192, V.193, F.194, C.216, T.217, G.218, S.220, G.237, I.239, Y.264, G.326, R.328, P.329, H.353, G.354, G.355, Y.356, G.357, Y.358, Q.359 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:I.239, D:R.328 Hydrogen bonds: D:A.31, D:G.32, D:S.34, D:S.34, D:S.34, D:K.55, D:H.56, D:H.56, D:E.64, D:C.66, D:S.67, D:S.67, D:G.71, D:N.73, D:N.73, D:N.73, D:F.194, D:F.194, D:S.220, D:H.353, D:G.354, D:G.357, D:Y.358, D:Q.359 Water bridges: D:G.35, D:R.328 pi-Cation interactions: D:R.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimekake, Y. et al., X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-11-11

Peptides

D-amino acid oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

D-amino acid oxidase