SMTL ID : 6uc1.1

Crystal structure of D678A GoxA soaked in glycine at pH 7.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.740, H.743 Chain B: R.423, G.801 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:I.802, B:I.802 Salt bridges: B:R.423, A:H.743 Hydrogen bonds: A:T.740, A:T.740 SO4.2: 2 residues within 4Å: Chain A: S.438, A.439 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.439 Water bridges: A:S.440 SO4.3: 5 residues within 4Å: Chain A: S.240, G.257, K.258, A.261, N.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.258, A:N.262 Water bridges: A:S.240, A:S.240 SO4.4: 4 residues within 4Å: Chain A: D.460, S.495, S.496, K.498 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.460, A:S.496 Water bridges: A:K.498 Salt bridges: A:K.498 SO4.5: 4 residues within 4Å: Chain A: E.795, N.796, P.797, G.798 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.795, A:G.798 SO4.8: 5 residues within 4Å: Chain A: R.423, G.801 Chain B: E.739, T.740, H.743 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:R.423, B:T.740 Salt bridges: A:R.423, B:H.743 Hydrogen bonds: B:T.740 SO4.9: 2 residues within 4Å: Chain B: H.730, S.731 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.731 Salt bridges: B:H.730 SO4.13: 6 residues within 4Å: Chain C: E.739, T.740, H.743 Chain D: R.423, S.427, G.801 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.739, C:T.740, C:T.740 Salt bridges: C:H.743, D:R.423 SO4.14: 4 residues within 4Å: Chain C: D.460, S.495, S.496, K.498 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.496, C:S.496 Salt bridges: C:K.498 SO4.18: 7 residues within 4Å: Chain C: R.423, S.427, G.801 Chain D: S.737, E.739, T.740, H.743 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Water bridges: C:G.801, D:E.739, D:E.739 Salt bridges: C:R.423, D:H.743 Hydrogen bonds: D:T.740 SO4.19: 3 residues within 4Å: Chain D: S.438, A.439, S.440 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.439 Water bridges: D:S.440, D:S.440 SO4.20: 4 residues within 4Å: Chain D: D.460, S.495, S.496, K.498 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.496 Salt bridges: D:K.498

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 7 residues within 4Å: Chain A: D.360, A.362, P.363, I.365, P.367, A.699, N.700 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.360, A:A.362, A:I.365, A:A.699, H2O.1 MG.10: 7 residues within 4Å: Chain B: D.360, A.362, P.363, I.365, P.367, A.699, N.700 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.360, B:A.362, B:I.365, B:A.699, H2O.15 MG.15: 7 residues within 4Å: Chain C: D.360, A.362, P.363, I.365, P.367, A.699, N.700 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.360, C:A.362, C:I.365, C:A.699, H2O.27 MG.21: 7 residues within 4Å: Chain D: D.360, A.362, P.363, I.365, P.367, A.699, N.700 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.360, D:A.362, D:I.365, D:A.699, H2O.37

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 12 residues within 4Å: Chain A: L.312, T.314, E.769, T.773, N.774, I.777 Chain D: L.312, T.314, E.769, T.773, N.774, I.777 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:N.774, D:N.774, D:N.774 Water bridges: A:T.773, D:T.773

4 x GLY: GLYCINE(Non-covalent)

GLY.11: 11 residues within 4Å: Chain A: F.316, H.583, P.584, A.678, S.681, C.682, W.696, W.697, Y.772 Chain B: Y.766, H.767 8 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: A:H.583, A:S.681, A:S.681, A:W.696, G.11, B:Y.766 Salt bridges: A:H.583, B:H.767 GLY.12: 11 residues within 4Å: Chain A: Y.766, H.767 Chain B: F.316, H.583, P.584, A.678, S.681, C.682, W.696, W.697, Y.772 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.583, B:S.681, B:S.681, A:Y.766 Water bridges: B:W.696 Salt bridges: B:H.583, A:H.767 GLY.16: 11 residues within 4Å: Chain C: Y.766, H.767 Chain D: F.316, H.583, P.584, G.585, S.681, C.682, W.696, W.697, Y.772 8 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: G.16, G.16, D:H.583, D:H.583, D:S.681, D:W.696 Salt bridges: D:H.583, C:H.767 GLY.17: 10 residues within 4Å: Chain C: F.316, H.583, P.584, A.678, S.681, C.682, W.696, W.697 Chain D: Y.766, H.767 7 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: D:Y.766, C:S.681, C:S.681, G.17 Salt bridges: D:H.767, C:H.583 Water bridges: C:W.696

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mamounis, K.J. et al., Kinetic and structural evidence that Asp-678 plays multiple roles in catalysis by the quinoprotein glycine oxidase. J.Biol.Chem. (2019)

Release Date

2019-10-23

Peptides

Uncharacterized protein GoxA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
D

D
C

Uncharacterized protein GoxA

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