SMTL ID : 3if9.1 (1 other biounit)

Crystal structure of Glycine Oxidase G51S/A54R/H244A mutant in complex with inhibitor glycolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.1: 4 residues within 4Å: Chain A: Y.259, R.315, R.342 Ligands: FAD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.259, A:R.315, A:R.342 Salt bridges: A:R.315, A:R.342 GOA.3: 4 residues within 4Å: Chain B: Y.259, R.315, R.342 Ligands: FAD.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.259, B:R.315, B:R.315, B:R.342 Salt bridges: B:R.315, B:R.342 GOA.5: 4 residues within 4Å: Chain C: Y.259, R.315, R.342 Ligands: FAD.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.315, C:R.342 Salt bridges: C:R.315, C:R.342 GOA.7: 4 residues within 4Å: Chain D: Y.259, R.315, R.342 Ligands: FAD.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.315, D:R.315, D:R.342 Salt bridges: D:R.315, D:R.342

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

FAD.2: 38 residues within 4Å: Chain A: I.23, G.24, G.25, G.26, I.27, I.28, F.46, E.47, S.48, R.54, T.55, T.56, A.58, A.59, A.60, G.61, M.62, P.186, V.187, A.214, S.215, G.216, W.218, M.221, F.222, G.237, C.239, Y.259, G.313, R.315, H.340, F.341, R.342, N.343, G.344, I.345, L.346 Ligands: GOA.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:R.315 Hydrogen bonds: A:G.25, A:I.28, A:S.48, A:S.48, A:T.55, A:T.56, A:T.56, A:A.60, A:G.61, A:M.62, A:M.62, A:V.187, A:V.187, A:G.216, A:F.341, A:G.344, A:I.345, A:L.346 Water bridges: A:G.26, A:G.26, A:E.47, A:G.53, A:R.54, A:T.55, A:T.55, A:T.56 FAD.4: 39 residues within 4Å: Chain B: I.23, G.24, G.25, G.26, I.27, I.28, F.46, E.47, S.48, R.54, T.55, T.56, A.58, A.59, A.60, G.61, M.62, P.186, V.187, A.214, S.215, G.216, W.218, M.221, F.222, C.239, Y.259, G.313, L.314, R.315, P.316, H.340, F.341, R.342, N.343, G.344, I.345, L.346 Ligands: GOA.3 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:A.60, B:M.62, B:I.345, B:I.345 Hydrogen bonds: B:G.25, B:I.28, B:S.48, B:T.55, B:T.56, B:T.56, B:A.60, B:V.187, B:V.187, B:G.216, B:H.340, B:F.341, B:G.344 Water bridges: B:G.26, B:G.26, B:R.54, B:T.55, B:V.217 FAD.6: 38 residues within 4Å: Chain C: I.23, G.24, G.25, G.26, I.27, I.28, F.46, E.47, S.48, R.54, T.55, T.56, A.58, A.59, A.60, G.61, M.62, P.186, V.187, A.214, S.215, G.216, W.218, M.221, F.222, G.237, C.239, Y.259, G.313, R.315, H.340, F.341, R.342, N.343, G.344, I.345, L.346 Ligands: GOA.5 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:R.315 Hydrogen bonds: C:G.25, C:I.28, C:S.48, C:S.48, C:T.55, C:T.55, C:T.56, C:T.56, C:A.60, C:G.61, C:M.62, C:M.62, C:V.187, C:V.187, C:G.216, C:F.341, C:G.344, C:I.345, C:L.346 Water bridges: C:G.26, C:G.26, C:E.47, C:G.53, C:R.54, C:T.56 FAD.8: 39 residues within 4Å: Chain D: I.23, G.24, G.25, G.26, I.27, I.28, F.46, E.47, S.48, R.54, T.55, T.56, A.58, A.59, A.60, G.61, M.62, P.186, V.187, A.214, S.215, G.216, W.218, M.221, F.222, C.239, Y.259, G.313, L.314, R.315, P.316, H.340, F.341, R.342, N.343, G.344, I.345, L.346 Ligands: GOA.7 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:A.60, D:M.62, D:I.345, D:I.345 Hydrogen bonds: D:G.25, D:I.28, D:S.48, D:T.55, D:T.55, D:T.56, D:A.60, D:V.187, D:V.187, D:G.216, D:Y.259, D:H.340, D:F.341, D:G.344 Water bridges: D:G.26, D:G.26, D:R.54, D:V.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedotti, M. et al., Glyphosate resistance by engineering the flavoenzyme glycine oxidase. J.Biol.Chem. (2009)

Release Date

2009-10-27

Peptides

Glycine oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glycine oxidase

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