SMTL ID : 1v5f.1

Crystal Structure of Pyruvate oxidase complexed with FAD and TPP, from Aerococcus viridans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.439, N.466 Ligands: TPP.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.439, H2O.2, H2O.78 MG.8: 3 residues within 4Å: Chain B: D.439, N.466 Ligands: TPP.14 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.439, H2O.565, H2O.641 MG.15: 3 residues within 4Å: Chain C: D.439, N.466 Ligands: TPP.21 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.439, H2O.1128, H2O.1204 MG.22: 3 residues within 4Å: Chain D: D.439, N.466 Ligands: TPP.28 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.439, H2O.1691, H2O.1767

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

SO4.2: 9 residues within 4Å: Chain A: I.472, K.475 Chain B: S.26, G.27, T.28, S.74, R.103, Q.114 Ligands: TPP.7 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.130 Chain C: H.124 Chain D: L.116, N.117 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: A.331, V.332, E.333, E.334 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: R.206, G.582, L.583, E.584 Ligand excluded by PLIP SO4.9: 9 residues within 4Å: Chain A: S.26, G.27, T.28, S.74, R.103, Q.114 Chain B: I.472, K.475 Ligands: TPP.14 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: R.130 Chain C: L.116, N.117 Chain D: H.124 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: A.331, V.332, E.333, E.334 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: R.206, G.582, L.583, E.584 Ligand excluded by PLIP SO4.16: 9 residues within 4Å: Chain C: I.472, K.475 Chain D: S.26, G.27, T.28, S.74, R.103, Q.114 Ligands: TPP.21 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain A: H.124 Chain B: L.116, N.117 Chain C: R.130 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain C: A.331, V.332, E.333, E.334 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: R.206, G.582, L.583, E.584 Ligand excluded by PLIP SO4.23: 9 residues within 4Å: Chain C: S.26, G.27, T.28, S.74, R.103, Q.114 Chain D: I.472, K.475 Ligands: TPP.28 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain A: L.116, N.117 Chain B: H.124 Chain D: R.130 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain D: A.331, V.332, E.333, E.334 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain D: R.206, G.582, L.583, E.584 Ligand excluded by PLIP

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

FAD.6: 28 residues within 4Å: Chain A: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, Q.391, S.408, P.409, A.412 Chain B: F.113 26 PLIP interactions: 24 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.257, A:A.412, B:F.113, B:F.113 Hydrogen bonds: A:I.213, A:G.214, A:T.236, A:T.236, A:G.237, A:T.254, A:V.257, A:S.277, A:N.278, A:I.299, A:D.317, A:A.318, A:P.409 Water bridges: A:R.153, A:N.278, A:N.278, A:N.278, A:N.278, A:N.278, A:D.300 Salt bridges: A:K.238, A:K.238 FAD.13: 28 residues within 4Å: Chain A: F.113 Chain B: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, Q.391, S.408, P.409, A.412 26 PLIP interactions: 2 interactions with chain A, 24 interactions with chain B Hydrophobic interactions: A:F.113, A:F.113, B:V.257, B:A.412 Hydrogen bonds: B:I.213, B:G.214, B:T.236, B:T.236, B:G.237, B:T.254, B:V.257, B:S.277, B:N.278, B:I.299, B:D.317, B:A.318, B:P.409 Water bridges: B:R.153, B:N.278, B:N.278, B:N.278, B:N.278, B:N.278, B:D.300 Salt bridges: B:K.238, B:K.238 FAD.20: 28 residues within 4Å: Chain C: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, Q.391, S.408, P.409, A.412 Chain D: F.113 25 PLIP interactions: 23 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.257, C:A.412, D:F.113, D:F.113 Hydrogen bonds: C:I.213, C:G.214, C:T.236, C:G.237, C:T.254, C:V.257, C:S.277, C:N.278, C:I.299, C:D.317, C:D.317, C:A.318, C:P.409 Water bridges: C:R.153, C:N.278, C:N.278, C:N.278, C:N.278, C:N.278 Salt bridges: C:K.238, C:K.238 FAD.27: 28 residues within 4Å: Chain C: F.113 Chain D: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, Q.391, S.408, P.409, A.412 25 PLIP interactions: 23 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.257, D:A.412, C:F.113, C:F.113 Hydrogen bonds: D:I.213, D:G.214, D:T.236, D:G.237, D:T.254, D:V.257, D:S.277, D:N.278, D:I.299, D:D.317, D:D.317, D:A.318, D:P.409 Water bridges: D:R.153, D:N.278, D:N.278, D:N.278, D:N.278, D:N.278 Salt bridges: D:K.238, D:K.238

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.7: 29 residues within 4Å: Chain A: N.84, V.386, G.387, N.388, S.389, A.412, T.413, M.414, G.438, D.439, G.440, A.441, M.444, N.466, Y.469, A.470, F.471, I.472 Chain B: I.24, P.25, S.26, E.51, S.74, P.77, G.78, H.81, Q.114 Ligands: MG.1, SO4.2 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.469, A:I.472, B:I.24, B:P.77 Hydrogen bonds: A:N.388, A:S.389, A:A.412, A:M.414, A:G.440, A:A.441, A:N.466, A:A.470, A:F.471, B:S.74, B:Q.114 Water bridges: A:G.387, A:T.390, A:G.438, A:D.439, A:D.439, A:N.466, A:E.468 TPP.14: 29 residues within 4Å: Chain A: I.24, P.25, S.26, E.51, S.74, P.77, G.78, H.81, Q.114 Chain B: N.84, V.386, G.387, N.388, S.389, A.412, T.413, M.414, G.438, D.439, G.440, A.441, M.444, N.466, Y.469, A.470, F.471, I.472 Ligands: MG.8, SO4.9 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.469, B:I.472, A:I.24, A:P.77 Hydrogen bonds: B:N.388, B:S.389, B:A.412, B:M.414, B:G.440, B:A.441, B:N.466, B:A.470, B:F.471, A:S.74, A:Q.114 Water bridges: B:G.387, B:T.390, B:G.438, B:D.439, B:D.439, B:N.466, B:E.468 TPP.21: 29 residues within 4Å: Chain C: N.84, V.386, G.387, N.388, S.389, A.412, T.413, M.414, G.438, D.439, G.440, A.441, M.444, N.466, Y.469, A.470, F.471, I.472 Chain D: I.24, P.25, S.26, E.51, S.74, P.77, G.78, H.81, Q.114 Ligands: MG.15, SO4.16 21 PLIP interactions: 17 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.469, C:I.472, D:I.24, D:P.77 Hydrogen bonds: C:N.388, C:S.389, C:A.412, C:M.414, C:G.440, C:A.441, C:A.470, C:F.471, D:S.74, D:Q.114 Water bridges: C:G.387, C:T.390, C:G.438, C:D.439, C:D.439, C:N.466, C:E.468 TPP.28: 29 residues within 4Å: Chain C: I.24, P.25, S.26, E.51, S.74, P.77, G.78, H.81, Q.114 Chain D: N.84, V.386, G.387, N.388, S.389, A.412, T.413, M.414, G.438, D.439, G.440, A.441, M.444, N.466, Y.469, A.470, F.471, I.472 Ligands: MG.22, SO4.23 21 PLIP interactions: 17 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.469, D:I.472, C:I.24, C:P.77 Hydrogen bonds: D:N.388, D:S.389, D:A.412, D:M.414, D:G.440, D:A.441, D:A.470, D:F.471, C:S.74, C:Q.114 Water bridges: D:G.387, D:T.390, D:G.438, D:D.439, D:D.439, D:N.466, D:E.468

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juan, E.C. 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

2005-06-28

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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