SMTL ID : 8jpw.1

Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-octamer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:R.105, A:E.595 Hydrogen bonds: A:A.74, A:G.75, A:A.77, A:A.97, A:R.105, A:A.130, A:M.131, A:R.132, A:R.132, A:M.362, A:M.362, A:S.427, A:E.623, A:I.632 Water bridges: A:G.78, A:E.96, A:G.104, A:R.105, A:H.624 Salt bridges: A:R.105, A:R.105 FAD.5: 38 residues within 4Å: Chain B: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:R.105, B:E.595 Hydrogen bonds: B:A.74, B:G.75, B:A.77, B:A.97, B:R.105, B:A.130, B:M.131, B:R.132, B:R.132, B:M.362, B:M.362, B:S.427, B:E.623, B:I.632 Water bridges: B:G.78, B:E.96, B:G.104, B:R.105, B:H.624 Salt bridges: B:R.105, B:R.105 FAD.9: 38 residues within 4Å: Chain C: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.10 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:R.105, C:E.595 Hydrogen bonds: C:A.74, C:G.75, C:A.77, C:A.97, C:R.105, C:A.130, C:M.131, C:R.132, C:R.132, C:M.362, C:M.362, C:S.427, C:E.623, C:I.632 Water bridges: C:G.78, C:E.96, C:G.104, C:R.105, C:H.624 Salt bridges: C:R.105, C:R.105 FAD.13: 38 residues within 4Å: Chain D: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.14 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:R.105, D:E.595 Hydrogen bonds: D:A.74, D:G.75, D:A.77, D:A.97, D:R.105, D:A.130, D:M.131, D:R.132, D:R.132, D:M.362, D:M.362, D:S.427, D:E.623, D:I.632 Water bridges: D:G.78, D:E.96, D:G.104, D:R.105, D:H.624 Salt bridges: D:R.105, D:R.105 FAD.17: 38 residues within 4Å: Chain E: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.18 23 PLIP interactions: 23 interactions with chain E Hydrophobic interactions: E:R.105, E:E.595 Hydrogen bonds: E:A.74, E:G.75, E:A.77, E:A.97, E:R.105, E:A.130, E:M.131, E:R.132, E:R.132, E:M.362, E:M.362, E:S.427, E:E.623, E:I.632 Water bridges: E:G.78, E:E.96, E:G.104, E:R.105, E:R.105 Salt bridges: E:R.105, E:R.105 FAD.21: 38 residues within 4Å: Chain F: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.22 23 PLIP interactions: 23 interactions with chain F Hydrophobic interactions: F:R.105, F:E.595 Hydrogen bonds: F:A.74, F:G.75, F:A.77, F:A.97, F:R.105, F:A.130, F:M.131, F:R.132, F:R.132, F:M.362, F:M.362, F:S.427, F:E.623, F:I.632 Water bridges: F:G.78, F:E.96, F:G.104, F:R.105, F:R.105 Salt bridges: F:R.105, F:R.105 FAD.25: 38 residues within 4Å: Chain G: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.26 23 PLIP interactions: 23 interactions with chain G Hydrophobic interactions: G:R.105, G:E.595 Hydrogen bonds: G:A.74, G:G.75, G:A.77, G:A.97, G:R.105, G:A.130, G:M.131, G:R.132, G:R.132, G:M.362, G:M.362, G:S.427, G:E.623, G:I.632 Water bridges: G:G.78, G:E.96, G:G.104, G:R.105, G:R.105 Salt bridges: G:R.105, G:R.105 FAD.29: 38 residues within 4Å: Chain H: V.72, G.73, A.74, G.75, I.76, A.77, L.95, E.96, A.97, N.98, G.103, G.104, R.105, I.106, A.128, G.129, A.130, M.131, R.132, Q.360, R.361, M.362, T.422, I.423, P.424, S.427, K.455, Y.540, W.586, Y.591, E.595, G.622, E.623, A.630, W.631, I.632, A.635 Ligands: AKG.30 23 PLIP interactions: 23 interactions with chain H Hydrophobic interactions: H:R.105, H:E.595 Hydrogen bonds: H:A.74, H:G.75, H:A.77, H:A.97, H:R.105, H:A.130, H:M.131, H:R.132, H:R.132, H:M.362, H:M.362, H:S.427, H:E.623, H:I.632 Water bridges: H:G.78, H:E.96, H:G.104, H:R.105, H:R.105 Salt bridges: H:R.105, H:R.105

8 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 9 residues within 4Å: Chain A: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.540 Hydrogen bonds: A:Y.522 Water bridges: A:M.131 Salt bridges: A:R.132, A:R.132 AKG.6: 9 residues within 4Å: Chain B: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.540 Hydrogen bonds: B:Y.522 Water bridges: B:M.131 Salt bridges: B:R.132, B:R.132 AKG.10: 9 residues within 4Å: Chain C: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.9 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.540 Hydrogen bonds: C:Y.522 Water bridges: C:M.131 Salt bridges: C:R.132, C:R.132 AKG.14: 9 residues within 4Å: Chain D: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.13 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.540 Hydrogen bonds: D:Y.522 Water bridges: D:M.131 Salt bridges: D:R.132, D:R.132 AKG.18: 9 residues within 4Å: Chain E: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.17 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.540 Water bridges: E:M.131 Salt bridges: E:R.132, E:R.132 AKG.22: 9 residues within 4Å: Chain F: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.21 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:Y.540 Water bridges: F:M.131 Salt bridges: F:R.132, F:R.132 AKG.26: 9 residues within 4Å: Chain G: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.25 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:Y.540 Water bridges: G:M.131 Salt bridges: G:R.132, G:R.132 AKG.30: 9 residues within 4Å: Chain H: M.131, R.132, G.324, Y.522, Y.540, E.595, A.630, W.631 Ligands: FAD.29 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:Y.540 Water bridges: H:M.131 Salt bridges: H:R.132, H:R.132

16 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.110, A:E.346, H2O.1 ZN.4: 1 residues within 4Å: Chain A: D.167 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.167 ZN.7: 3 residues within 4Å: Chain B: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.110, B:E.346, H2O.8 ZN.8: 1 residues within 4Å: Chain B: D.167 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.167 ZN.11: 3 residues within 4Å: Chain C: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.110, C:E.346, H2O.15 ZN.12: 1 residues within 4Å: Chain C: D.167 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.167 ZN.15: 3 residues within 4Å: Chain D: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.110, D:E.346, H2O.22 ZN.16: 1 residues within 4Å: Chain D: D.167 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.167 ZN.19: 3 residues within 4Å: Chain E: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.110, E:E.346, H2O.30 ZN.20: 1 residues within 4Å: Chain E: D.167 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.167 ZN.23: 3 residues within 4Å: Chain F: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.110, F:E.346, H2O.37 ZN.24: 1 residues within 4Å: Chain F: D.167 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.167 ZN.27: 3 residues within 4Å: Chain G: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.110, G:E.346, H2O.44 ZN.28: 1 residues within 4Å: Chain G: D.167 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.167 ZN.31: 3 residues within 4Å: Chain H: H.110, K.112, E.346 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.110, H:E.346, H2O.51 ZN.32: 1 residues within 4Å: Chain H: D.167 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamaguchi, H. et al., Development of a novel single-chain l-glutamate oxidase from Streptomyces sp. X-119-6 by inserting flexible linkers. Enzyme.Microb.Technol. (2023)

Release Date

2023-08-09

Peptides

L-glutamate oxidase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

L-glutamate oxidase