- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.09 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x PYR: PYRUVIC ACID(Non-covalent)
- 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: TDM.8
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:G.35, C:S.36, C:A.83, C:Q.122, A:E.483
- Water bridges: 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: TDM.19
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:G.35, D:S.36, D:Q.122, D:Q.122
PO4.23: 8 residues within 4Å:- Chain A: G.34, G.35, S.36, S.82, Q.122
- Chain C: I.480, E.483
- Ligands: TDM.28
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:G.35, A:S.36, A:A.83, A:Q.122, C:E.483
- Water bridges: A:Q.122
PO4.33: 8 residues within 4Å:- Chain B: G.34, G.35, S.36, S.82, Q.122
- Chain D: I.480, E.483
- Ligands: TDM.39
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.35, B:S.36, B:Q.122, B:Q.122
- 16 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 6 residues within 4Å:- Chain A: A.23, W.24, K.75, Y.158, A.186, Y.189
Ligand excluded by PLIPGOL.5: 6 residues within 4Å:- Chain A: K.433, P.437, E.438, P.466, A.533, Q.534
Ligand excluded by PLIPGOL.6: 6 residues within 4Å:- Chain A: R.156, H.160
- Chain B: N.286, K.311, K.314
- Chain D: D.119
Ligand excluded by PLIPGOL.10: 3 residues within 4Å:- Chain A: T.487, Q.489
- Chain C: W.174
Ligand excluded by PLIPGOL.14: 8 residues within 4Å:- Chain B: G.25, V.26, D.27, H.28, D.69, T.73, K.75, N.435
Ligand excluded by PLIPGOL.15: 4 residues within 4Å:- Chain B: A.569, F.570, R.573, Y.574
Ligand excluded by PLIPGOL.16: 7 residues within 4Å:- Chain B: K.433, P.437, E.438, R.439, P.466, A.533, Q.534
Ligand excluded by PLIPGOL.17: 4 residues within 4Å:- Chain B: R.224, I.250, P.409, R.412
Ligand excluded by PLIPGOL.24: 6 residues within 4Å:- Chain C: A.23, W.24, K.75, Y.158, A.186, Y.189
Ligand excluded by PLIPGOL.25: 6 residues within 4Å:- Chain C: K.433, P.437, E.438, P.466, A.533, Q.534
Ligand excluded by PLIPGOL.26: 6 residues within 4Å:- Chain B: D.119
- Chain C: R.156, H.160
- Chain D: N.286, K.311, K.314
Ligand excluded by PLIPGOL.30: 3 residues within 4Å:- Chain A: W.174
- Chain C: T.487, Q.489
Ligand excluded by PLIPGOL.34: 8 residues within 4Å:- Chain D: G.25, V.26, D.27, H.28, D.69, T.73, K.75, N.435
Ligand excluded by PLIPGOL.35: 4 residues within 4Å:- Chain D: A.569, F.570, R.573, Y.574
Ligand excluded by PLIPGOL.36: 7 residues within 4Å:- Chain D: K.433, P.437, E.438, R.439, P.466, A.533, Q.534
Ligand excluded by PLIPGOL.37: 4 residues within 4Å:- Chain D: R.224, I.250, P.409, R.412
Ligand excluded by PLIP- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.7: 4 residues within 4Å:- Chain A: D.447, N.474, Q.476
- Ligands: TDM.8
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.447, A:Q.476, H2O.32
MG.18: 4 residues within 4Å:- Chain B: D.447, N.474, Q.476
- Ligands: TDM.19
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.447, B:Q.476, H2O.69
MG.27: 4 residues within 4Å:- Chain C: D.447, N.474, Q.476
- Ligands: TDM.28
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.447, C:Q.476, H2O.107
MG.38: 4 residues within 4Å:- Chain D: D.447, N.474, Q.476
- Ligands: TDM.39
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.447, D:Q.476, H2O.143
- 4 x TDM: 2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
TDM.8: 27 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: PO4.3, MG.7, FAD.9
23 PLIP interactions:18 interactions with chain A, 5 interactions with chain C- Hydrophobic interactions: A:V.394, A:Y.477, A:F.479, C:I.32, C:P.85
- Hydrogen bonds: A:D.396, A:A.420, A:M.422, A:G.446, A:G.448, A:G.449, A:N.474, A:Q.476, A:G.478, A:F.479, C:S.82, C:Q.122, C:Q.122
- Water bridges: A:I.397, A:I.397, A:G.446, A:D.447, A:D.447
TDM.19: 27 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: PO4.13, MG.18, FAD.20
23 PLIP interactions:18 interactions with chain B, 5 interactions with chain D- Hydrophobic interactions: B:V.394, B:Y.477, B:F.479, D:I.32, D:P.85
- Hydrogen bonds: B:D.396, B:A.420, B:M.422, B:G.446, B:G.448, B:G.449, B:N.474, B:N.474, B:G.478, B:F.479, D:S.82, D:Q.122
- Water bridges: B:I.397, B:G.446, B:G.446, B:D.447, B:D.447, D:Q.122
TDM.28: 27 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: PO4.23, MG.27, FAD.29
24 PLIP interactions:19 interactions with chain C, 5 interactions with chain A- Hydrophobic interactions: C:V.394, C:Y.477, C:F.479, A:I.32, A:P.85
- Hydrogen bonds: C:D.396, C:D.396, C:A.420, C:M.422, C:G.446, C:G.448, C:G.449, C:N.474, C:Q.476, C:G.478, C:F.479, A:S.82, A:Q.122, A:Q.122
- Water bridges: C:I.397, C:I.397, C:G.446, C:D.447, C:D.447
TDM.39: 27 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: PO4.33, MG.38, FAD.40
24 PLIP interactions:5 interactions with chain B, 19 interactions with chain D- Hydrophobic interactions: B:I.32, B:P.85, D:V.394, D:Y.477, D:F.479
- Hydrogen bonds: B:S.82, B:Q.122, D:D.396, D:D.396, D:A.420, D:M.422, D:G.446, D:G.448, D:G.449, D:N.474, D:N.474, D:G.478, D:F.479
- Water bridges: B:Q.122, D:I.397, D:G.446, D:G.446, D:D.447, D:D.447
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
FAD.9: 33 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
- Ligands: PYR.2, TDM.8
25 PLIP interactions:23 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:N.417
- Salt bridges: A:H.101
FAD.20: 32 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
- Chain D: F.121
- Ligands: PYR.12, TDM.19
25 PLIP interactions:23 interactions with chain B, 2 interactions with chain D- Hydrophobic interactions: B:Y.245, B:V.265, B:V.394, 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:N.286, B:N.286, B:R.315, B:N.417
- Salt bridges: B:H.101
FAD.29: 33 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
- Ligands: PYR.22, TDM.28
28 PLIP interactions:26 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:N.417
- Salt bridges: C:H.101
FAD.40: 32 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
- Ligands: PYR.32, TDM.39
25 PLIP interactions:23 interactions with chain D, 2 interactions with chain B- Hydrophobic interactions: D:Y.245, D:V.265, D:V.394, 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:N.286, D:N.286, D:R.315, D:N.417
- Salt bridges: D:H.101
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Meyer, D. et al., Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin. Proc.Natl.Acad.Sci.USA (2012)
- Release Date
- 2012-06-20
- Peptides
- Pyruvate oxidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.09 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x PYR: PYRUVIC ACID(Non-covalent)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 16 x GOL: GLYCEROL(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x TDM: 2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Meyer, D. et al., Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin. Proc.Natl.Acad.Sci.USA (2012)
- Release Date
- 2012-06-20
- Peptides
- Pyruvate oxidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B