SMTL ID : 2dji.1

Crystal Structure of Pyruvate Oxidase from Aerococcus viridans containing FAD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.131 Chain C: H.125 Chain D: L.117, N.118 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: A.332, V.333, E.334, E.335 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.207, G.583, L.584, E.585 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain A: G.388, M.415, G.439, D.440, G.441, A.442, E.469, Y.470 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain B: R.131 Chain C: L.117, N.118 Chain D: H.125 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain B: A.332, V.333, E.334, E.335 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: R.207, G.583, L.584, E.585 Ligand excluded by PLIP SO4.9: 8 residues within 4Å: Chain B: G.388, M.415, G.439, D.440, G.441, A.442, E.469, Y.470 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: H.125 Chain B: L.117, N.118 Chain C: R.131 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain C: A.332, V.333, E.334, E.335 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain C: R.207, G.583, L.584, E.585 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain C: G.388, M.415, G.439, D.440, G.441, A.442, E.469, Y.470 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: L.117, N.118 Chain B: H.125 Chain D: R.131 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain D: A.332, V.333, E.334, E.335 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain D: R.207, G.583, L.584, E.585 Ligand excluded by PLIP SO4.19: 8 residues within 4Å: Chain D: G.388, M.415, G.439, D.440, G.441, A.442, E.469, Y.470 Ligand excluded by PLIP

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

FAD.5: 30 residues within 4Å: Chain A: G.213, I.214, G.215, T.237, G.238, K.239, S.254, T.255, Y.256, R.257, V.258, G.277, S.278, N.279, F.280, P.281, F.282, D.299, I.300, D.301, M.304, G.317, D.318, A.319, V.387, Q.392, S.409, P.410, A.413 Chain B: F.114 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.258, A:V.387, A:A.413, B:F.114, B:F.114 Hydrogen bonds: A:I.214, A:G.215, A:T.237, A:T.237, A:G.238, A:T.255, A:V.258, A:S.278, A:N.279, A:I.300, A:D.318, A:A.319, A:P.410 Water bridges: A:K.239, A:K.239, A:K.239, A:N.279, A:N.279, A:N.279, A:N.279, A:D.301, A:D.301 Salt bridges: A:K.239, A:K.239 FAD.10: 30 residues within 4Å: Chain A: F.114 Chain B: G.213, I.214, G.215, T.237, G.238, K.239, S.254, T.255, Y.256, R.257, V.258, G.277, S.278, N.279, F.280, P.281, F.282, D.299, I.300, D.301, M.304, G.317, D.318, A.319, V.387, Q.392, S.409, P.410, A.413 29 PLIP interactions: 27 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.258, B:V.387, B:A.413, A:F.114, A:F.114 Hydrogen bonds: B:I.214, B:G.215, B:T.237, B:T.237, B:G.238, B:T.255, B:V.258, B:S.278, B:N.279, B:I.300, B:D.318, B:A.319, B:P.410 Water bridges: B:K.239, B:K.239, B:K.239, B:N.279, B:N.279, B:N.279, B:N.279, B:D.301, B:D.301 Salt bridges: B:K.239, B:K.239 FAD.15: 30 residues within 4Å: Chain C: G.213, I.214, G.215, T.237, G.238, K.239, S.254, T.255, Y.256, R.257, V.258, G.277, S.278, N.279, F.280, P.281, F.282, D.299, I.300, D.301, M.304, G.317, D.318, A.319, V.387, Q.392, S.409, P.410, A.413 Chain D: F.114 28 PLIP interactions: 26 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.258, C:V.387, C:A.413, D:F.114, D:F.114 Hydrogen bonds: C:I.214, C:G.215, C:T.237, C:G.238, C:T.255, C:V.258, C:S.278, C:N.279, C:I.300, C:D.318, C:D.318, C:A.319, C:P.410 Water bridges: C:K.239, C:K.239, C:K.239, C:N.279, C:N.279, C:N.279, C:N.279, C:N.279 Salt bridges: C:K.239, C:K.239 FAD.20: 30 residues within 4Å: Chain C: F.114 Chain D: G.213, I.214, G.215, T.237, G.238, K.239, S.254, T.255, Y.256, R.257, V.258, G.277, S.278, N.279, F.280, P.281, F.282, D.299, I.300, D.301, M.304, G.317, D.318, A.319, V.387, Q.392, S.409, P.410, A.413 28 PLIP interactions: 26 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.258, D:V.387, D:A.413, C:F.114, C:F.114 Hydrogen bonds: D:I.214, D:G.215, D:T.237, D:G.238, D:T.255, D:V.258, D:S.278, D:N.279, D:I.300, D:D.318, D:D.318, D:A.319, D:P.410 Water bridges: D:K.239, D:K.239, D:K.239, D:N.279, D:N.279, D:N.279, D:N.279, D:N.279 Salt bridges: D:K.239, D:K.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juan, E.C.M. et al., The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis. Acta Crystallogr.,Sect.F (2007)

Release Date

2007-05-29

Peptides

Pyruvate oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Pyruvate oxidase

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