- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.13 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 12 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 6 residues within 4Å:- Chain A: A.23, W.24, K.75, Y.158, A.186, Y.189
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:A.23, A:W.24
- Water bridges: A:Y.158, A:Y.189
GOL.5: 7 residues within 4Å:- Chain A: K.433, P.437, E.438, R.439, P.466, A.533, Q.534
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.438, A:Q.534
- Water bridges: A:K.433, A:E.438, A:E.438
GOL.6: 3 residues within 4Å:- Chain A: W.174
- Chain C: T.487, Q.489
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:Q.489, A:W.174
- Water bridges: C:D.486
GOL.9: 4 residues within 4Å:- Chain A: R.224, I.250, P.409, R.412
3 PLIP interactions:3 interactions with chain A- Water bridges: A:R.224, A:R.224, A:R.224
GOL.16: 4 residues within 4Å:- Chain B: A.569, F.570, R.573, Y.574
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:R.573
- Water bridges: B:E.485, B:E.485, B:F.570
GOL.17: 4 residues within 4Å:- Chain B: R.224, I.250, P.409, R.412
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:P.409, B:R.412
GOL.20: 6 residues within 4Å:- Chain C: A.23, W.24, K.75, Y.158, A.186, Y.189
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:A.23, C:W.24, C:Y.158
- Water bridges: C:Y.158, C:Y.189
GOL.23: 7 residues within 4Å:- Chain C: K.433, P.437, E.438, R.439, P.466, A.533, Q.534
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:E.438, C:Q.534
- Water bridges: C:K.433
GOL.24: 3 residues within 4Å:- Chain A: T.487, Q.489
- Chain C: W.174
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain A- Hydrogen bonds: C:W.174, A:Q.489
- Water bridges: A:D.486
GOL.27: 4 residues within 4Å:- Chain C: R.224, I.250, P.409, R.412
3 PLIP interactions:3 interactions with chain C- Water bridges: C:R.224, C:R.224, C:R.224
GOL.34: 4 residues within 4Å:- Chain D: A.569, F.570, R.573, Y.574
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:R.573, D:Y.574
- Water bridges: D:E.485, D:F.570
GOL.35: 4 residues within 4Å:- Chain D: R.224, I.250, P.409, R.412
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:P.409, D:R.412
- 8 x PYR: PYRUVIC ACID(Non-covalent)
PYR.3: 6 residues within 4Å:- Chain A: L.555, R.556, L.557, D.558, M.561, S.562
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.555
- Hydrogen bonds: A:L.557, A:D.558
- Salt bridges: A:R.556
PYR.4: 7 residues within 4Å:- Chain A: N.263, R.264, F.289, F.479, E.483
- Chain C: F.121
- Ligands: FAD.1
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain C- Hydrophobic interactions: A:F.289, C:F.121
- Hydrogen bonds: A:N.263, A:N.263, A:E.483
- Salt bridges: A:R.264
PYR.12: 6 residues within 4Å:- Chain B: L.555, R.556, L.557, D.558, M.561, S.562
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:M.561
- Hydrogen bonds: B:L.557, B:D.558
PYR.13: 7 residues within 4Å:- Chain B: N.263, R.264, F.289, F.479, E.483
- Chain D: F.121
- Ligands: FAD.11
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain D- Hydrophobic interactions: B:F.289, D:F.121
- Hydrogen bonds: B:N.263, B:N.263, B:E.483
- Salt bridges: B:R.264
PYR.21: 6 residues within 4Å:- Chain C: L.555, R.556, L.557, D.558, M.561, S.562
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:L.555
- Hydrogen bonds: C:L.557, C:D.558
- Water bridges: C:E.272
- Salt bridges: C:R.556
PYR.22: 7 residues within 4Å:- Chain A: F.121
- Chain C: N.263, R.264, F.289, F.479, E.483
- Ligands: FAD.19
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: C:F.289, A:F.121
- Hydrogen bonds: C:N.263, C:N.263
- Salt bridges: C:R.264
PYR.30: 6 residues within 4Å:- Chain D: L.555, R.556, L.557, D.558, M.561, S.562
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:M.561
- Hydrogen bonds: D:L.557, D:D.558
- Water bridges: D:E.272
PYR.31: 7 residues within 4Å:- Chain B: F.121
- Chain D: N.263, R.264, F.289, F.479, E.483
- Ligands: FAD.29
5 PLIP interactions:1 interactions with chain B, 4 interactions with chain D- Hydrophobic interactions: B:F.121, D:F.289
- Hydrogen bonds: D:N.263, D:N.263
- Salt bridges: D:R.264
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.7: 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:Q.122, A:E.483
- Water bridges: C:S.82, C:Q.122
PO4.15: 8 residues within 4Å:- Chain B: I.480, E.483
- Chain D: G.34, G.35, S.36, S.82, Q.122
- Ligands: TDM.14
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:G.35, D:S.36, D:Q.122
- Water bridges: D:G.35, D:Q.122
PO4.25: 8 residues within 4Å:- Chain A: G.34, G.35, S.36, S.82, Q.122
- Chain C: I.480, E.483
- Ligands: TDM.26
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
PO4.33: 8 residues within 4Å:- Chain B: G.34, G.35, S.36, S.82, Q.122
- Chain D: I.480, E.483
- Ligands: TDM.32
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.35, B:S.36, B:Q.122
- Water bridges: B:G.35, B:Q.122
- 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: FAD.1, PO4.7, MG.10
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.14: 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: FAD.11, PO4.15, MG.18
24 PLIP interactions:19 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:D.447, B:G.448, B:G.449, B:N.474, B:N.474, B:G.478, B:F.479, D:S.82, D:Q.122, D:Q.122
- Water bridges: B:I.397, B:G.446, B:G.446, B:D.447, B:D.447
TDM.26: 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: FAD.19, PO4.25, MG.28
24 PLIP interactions:18 interactions with chain C, 6 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: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, A:E.59
TDM.32: 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: FAD.29, PO4.33, MG.36
23 PLIP interactions:5 interactions with chain B, 18 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, B:Q.122, 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: D:I.397, D:G.446, D:G.446, D:D.447, D:D.447
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.10: 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.4
MG.18: 4 residues within 4Å:- Chain B: D.447, N.474, Q.476
- Ligands: TDM.14
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.447, B:Q.476, H2O.38
MG.28: 4 residues within 4Å:- Chain C: D.447, N.474, Q.476
- Ligands: TDM.26
3 PLIP interactions:2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.447, C:Q.476, H2O.68
MG.36: 4 residues within 4Å:- Chain D: D.447, N.474, Q.476
- Ligands: TDM.32
3 PLIP interactions:2 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.447, D:Q.476, H2O.102
- 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 1.13 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 12 x GOL: GLYCEROL(Non-functional Binders)
- 8 x PYR: PYRUVIC ACID(Non-covalent)
- 4 x PO4: PHOSPHATE ION(Non-functional Binders)
- 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 MG: MAGNESIUM ION(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