SMTL ID : 4kgd.1

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 31 residues within 4Å: Chain A: H.101, G.220, I.221, G.222, T.244, Y.245, P.246, S.261, A.262, N.263, R.264, V.265, G.284, N.285, N.286, Y.287, P.288, F.289, D.306, I.307, D.308, K.311, A.324, D.325, A.326, V.394, N.398, S.416, N.417, A.420 Chain C: F.121 27 PLIP interactions: 25 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.245, A:V.265, A:V.394, A:A.420, C:F.121, C:F.121 Hydrogen bonds: A:I.221, A:G.222, A:T.244, A:Y.245, A:A.262, A:N.263, A:R.264, A:V.265, A:N.285, A:N.286, A:I.307, A:D.325, A:A.326, A:N.417 Water bridges: A:A.262, A:N.286, A:N.286, A:D.308, A:K.311, A:N.417 Salt bridges: A:H.101 FAD.10: 31 residues within 4Å: Chain B: H.101, G.220, I.221, G.222, T.244, Y.245, P.246, S.261, A.262, N.263, R.264, V.265, G.284, N.285, N.286, Y.287, P.288, F.289, D.306, I.307, D.308, K.311, A.324, D.325, A.326, V.394, N.398, S.416, N.417, A.420 Chain D: F.121 29 PLIP interactions: 27 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.245, B:V.265, B:V.394, B:A.420, D:F.121, D:F.121 Hydrogen bonds: B:I.221, B:G.222, B:T.244, B:T.244, B:Y.245, B:A.262, B:N.263, B:R.264, B:V.265, B:N.285, B:N.286, B:I.307, B:D.325, B:A.326, B:N.417 Water bridges: B:A.262, B:N.286, B:N.286, B:D.308, B:K.311, B:R.315, B:N.417 Salt bridges: B:H.101 FAD.19: 31 residues within 4Å: Chain A: F.121 Chain C: H.101, G.220, I.221, G.222, T.244, Y.245, P.246, S.261, A.262, N.263, R.264, V.265, G.284, N.285, N.286, Y.287, P.288, F.289, D.306, I.307, D.308, K.311, A.324, D.325, A.326, V.394, N.398, S.416, N.417, A.420 30 PLIP interactions: 28 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:Y.245, C:V.265, C:V.394, C:A.420, A:F.121, A:F.121 Hydrogen bonds: C:I.221, C:G.222, C:T.244, C:T.244, C:Y.245, C:A.262, C:N.263, C:R.264, C:V.265, C:N.285, C:N.286, C:I.307, C:D.325, C:D.325, C:A.326, C:N.417 Water bridges: C:A.262, C:N.286, C:N.286, C:N.286, C:D.308, C:D.308, C:N.417 Salt bridges: C:H.101 FAD.28: 31 residues within 4Å: Chain B: F.121 Chain D: H.101, G.220, I.221, G.222, T.244, Y.245, P.246, S.261, A.262, N.263, R.264, V.265, G.284, N.285, N.286, Y.287, P.288, F.289, D.306, I.307, D.308, K.311, A.324, D.325, A.326, V.394, N.398, S.416, N.417, A.420 29 PLIP interactions: 27 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.245, D:V.265, D:V.394, D:A.420, B:F.121, B:F.121 Hydrogen bonds: D:I.221, D:G.222, D:T.244, D:Y.245, D:A.262, D:N.263, D:R.264, D:V.265, D:N.285, D:N.286, D:I.307, D:D.325, D:D.325, D:A.326, D:N.417 Water bridges: D:A.262, D:N.286, D:N.286, D:D.308, D:D.308, D:R.315, D:N.417 Salt bridges: D:H.101

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.447, N.474, Q.476 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:Q.476, H2O.1 MG.11: 4 residues within 4Å: Chain B: D.447, N.474, Q.476 Ligands: TPP.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:Q.476, H2O.37 MG.20: 4 residues within 4Å: Chain C: D.447, N.474, Q.476 Ligands: TPP.22 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.447, C:Q.476, H2O.74 MG.29: 4 residues within 4Å: Chain D: D.447, N.474, Q.476 Ligands: TPP.30 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.447, D:Q.476, H2O.110

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: I.480, E.483 Chain C: G.34, G.35, S.36, S.82, Q.122 Ligands: TPP.4 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.35, C:S.36, C:Q.122, A:E.483 Water bridges: C:S.82, C:Q.122 PO4.13: 8 residues within 4Å: Chain B: I.480, E.483 Chain D: G.34, G.35, S.36, S.82, Q.122 Ligands: TPP.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.35, D:S.36, D:Q.122 Water bridges: D:S.82, D:Q.122 PO4.21: 8 residues within 4Å: Chain A: G.34, G.35, S.36, S.82, Q.122 Chain C: I.480, E.483 Ligands: TPP.22 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.35, A:S.36, A:Q.122, C:E.483 Water bridges: A:S.82, A:Q.122 PO4.31: 8 residues within 4Å: Chain B: G.34, G.35, S.36, S.82, Q.122 Chain D: I.480, E.483 Ligands: TPP.30 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.35, B:S.36, B:Q.122 Water bridges: B:S.82, B:Q.122

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 26 residues within 4Å: Chain A: V.394, G.395, D.396, A.420, M.422, G.446, D.447, G.448, G.449, M.452, N.474, Q.476, Y.477, G.478, F.479, I.480 Chain C: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Ligands: MG.2, PO4.3 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:Y.477, C:I.32, C:P.85 Hydrogen bonds: A:D.396, A:A.420, A:M.422, A:G.448, A:G.449, A:N.474, A:G.478, A:F.479, C:S.82 Water bridges: A:I.397, A:I.397, A:G.446, A:D.447, A:D.447, C:Q.122, C:Q.122 TPP.12: 26 residues within 4Å: Chain B: V.394, G.395, D.396, A.420, M.422, G.446, D.447, G.448, G.449, M.452, N.474, Q.476, Y.477, G.478, F.479, I.480 Chain D: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Ligands: MG.11, PO4.13 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:Y.477, D:I.32, D:P.85 Hydrogen bonds: B:D.396, B:A.420, B:M.422, B:G.448, B:G.449, B:N.474, B:G.478, B:F.479, D:S.82 Water bridges: B:D.393, B:I.397, B:G.446, B:G.446, B:D.447, B:D.447, D:Q.122 TPP.22: 26 residues within 4Å: Chain A: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Chain C: V.394, G.395, D.396, A.420, M.422, G.446, D.447, G.448, G.449, M.452, N.474, Q.476, Y.477, G.478, F.479, I.480 Ligands: MG.20, PO4.21 20 PLIP interactions: 15 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:Y.477, A:I.32, A:P.85 Hydrogen bonds: C:D.396, C:D.396, C:A.420, C:M.422, C:G.448, C:G.449, C:N.474, C:G.478, C:F.479, A:S.82 Water bridges: C:I.397, C:I.397, C:G.446, C:D.447, C:D.447, A:Q.122, A:Q.122 TPP.30: 26 residues within 4Å: Chain B: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Chain D: V.394, G.395, D.396, A.420, M.422, G.446, D.447, G.448, G.449, M.452, N.474, Q.476, Y.477, G.478, F.479, I.480 Ligands: MG.29, PO4.31 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:Y.477, B:I.32, B:P.85 Hydrogen bonds: D:D.396, D:D.396, D:A.420, D:M.422, D:G.448, D:G.449, D:N.474, D:G.478, D:F.479, B:S.82 Water bridges: D:I.397, D:G.446, D:G.446, D:D.447, D:D.447, B:Q.122

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: A.23, W.24, K.75, Y.158, A.186, Y.189 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: K.433, P.437, E.438, P.466, A.533, Q.534 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: W.174 Chain C: T.487, Q.489 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: R.264, E.483, D.486, E.553 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: K.433, P.437, E.438, R.439, P.466, A.533, Q.534 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain B: W.174 Chain D: T.487 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: A.569, F.570, R.573, Y.574 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain B: P.409, S.410, N.411, R.412, Y.436, R.439 Ligands: GOL.18 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: R.224, I.250, P.409, R.412 Ligands: GOL.17 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain C: A.23, W.24, K.75, Y.158, A.186, Y.189 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: K.433, P.437, E.438, P.466, A.533, Q.534 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain A: T.487, Q.489 Chain C: W.174 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain C: R.264, E.483, D.486, E.553 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain D: K.433, P.437, E.438, R.439, P.466, A.533, Q.534 Ligand excluded by PLIP GOL.33: 2 residues within 4Å: Chain B: T.487 Chain D: W.174 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain D: A.569, F.570, R.573, Y.574 Ligand excluded by PLIP GOL.35: 7 residues within 4Å: Chain D: P.409, S.410, N.411, R.412, Y.436, R.439 Ligands: GOL.36 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain D: R.224, I.250, P.409, R.412 Ligands: GOL.35 Ligand excluded by PLIP

2 x K: POTASSIUM ION(Non-covalent)

K.9: 5 residues within 4Å: Chain A: M.452, Q.455 Chain C: M.452, Q.455 Ligands: K.27 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:M.452, A:M.452, H2O.1, H2O.74 K.27: 5 residues within 4Å: Chain A: M.452, Q.455 Chain C: M.452, Q.455 Ligands: K.9 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:M.452, A:M.452, H2O.1, H2O.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, D. et al., Observation of a stable carbene at the active site of a thiamin enzyme. Nat.Chem.Biol. (2013)

Release Date

2013-06-12

Peptides

Pyruvate oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate oxidase

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