- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.96 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
NA.2: 5 residues within 4Å:- Chain A: M.452, Q.455
- Chain C: M.452, Q.455
- Ligands: NA.12
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:M.452, C:Q.455
- Water bridges: A:Q.455
NA.6: 5 residues within 4Å:- Chain B: M.452, Q.455
- Chain D: M.452, Q.455
- Ligands: NA.16
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain B- Hydrogen bonds: D:Q.455, D:Q.455, B:Q.455
NA.12: 5 residues within 4Å:- Chain A: M.452, Q.455
- Chain C: M.452, Q.455
- Ligands: NA.2
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:Q.455, C:M.452
- Water bridges: C:Q.455
NA.16: 5 residues within 4Å:- Chain B: M.452, Q.455
- Chain D: M.452, Q.455
- Ligands: NA.6
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:Q.455, B:Q.455, D:Q.455
- 4 x TDL: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)
TDL.3: 31 residues within 4Å:- Chain A: V.394, G.395, D.396, A.420, T.421, M.422, G.446, D.447, G.448, G.449, M.452, N.474, Q.476, Y.477, G.478, W.479, I.480, E.483
- Chain C: I.32, P.33, G.34, G.35, E.59, S.82, P.85, G.86, H.89, F.121, Q.122
- Ligands: MG.1, FAD.4
25 PLIP interactions:18 interactions with chain A, 7 interactions with chain C- Hydrophobic interactions: A:V.394, A:Y.477, C:I.32, C:P.85, C:F.121
- Hydrogen bonds: A:D.396, A:D.396, A:A.420, A:M.422, A:G.446, A:G.448, A:G.449, A:N.474, A:G.478, A:W.479, A:W.479, C:G.35, C:S.82, C:Q.122
- Water bridges: A:I.397, A:G.446, A:G.446, A:D.447, A:D.447, C:S.36
TDL.8: 30 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, W.479, I.480, E.483
- Chain D: I.32, P.33, G.34, G.35, E.59, S.82, P.85, G.86, H.89, F.121, Q.122
- Ligands: MG.7, FAD.9
27 PLIP interactions:19 interactions with chain B, 8 interactions with chain D- Hydrophobic interactions: B:V.394, B:Y.477, D:I.32, D:P.85, D:F.121
- Hydrogen bonds: B:D.396, B:D.396, B:A.420, B:M.422, B:G.446, B:G.448, B:G.449, B:N.474, B:G.478, B:W.479, B:W.479, D:G.35, D:S.82, D:Q.122
- Water bridges: B:D.393, B:I.397, B:G.446, B:G.446, B:D.447, B:D.447, D:S.36, D:E.59
TDL.13: 31 residues within 4Å:- Chain A: I.32, P.33, G.34, G.35, E.59, S.82, P.85, G.86, H.89, F.121, Q.122
- Chain C: V.394, G.395, D.396, A.420, T.421, M.422, G.446, D.447, G.448, G.449, M.452, N.474, Q.476, Y.477, G.478, W.479, I.480, E.483
- Ligands: MG.11, FAD.14
28 PLIP interactions:20 interactions with chain C, 8 interactions with chain A- Hydrophobic interactions: C:V.394, C:Y.477, A:I.32, A:P.85, A:F.121
- Hydrogen bonds: C:D.396, 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:G.478, C:W.479, C:W.479, A:G.35, A:S.82, A:Q.122
- Water bridges: C:D.393, C:I.397, C:G.446, C:G.446, C:D.447, C:D.447, A:S.36, A:E.59
TDL.18: 30 residues within 4Å:- Chain B: I.32, P.33, G.34, G.35, E.59, S.82, P.85, G.86, H.89, F.121, 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, W.479, I.480, E.483
- Ligands: MG.17, FAD.19
26 PLIP interactions:19 interactions with chain D, 7 interactions with chain B- Hydrophobic interactions: D:V.394, D:Y.477, B:I.32, B:P.85, B:F.121
- Hydrogen bonds: D:D.396, 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:G.478, D:W.479, D:W.479, B:G.35, B:S.82, B:Q.122
- Water bridges: D:I.397, D:G.446, D:G.446, D:D.447, D:D.447, B:S.36
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
FAD.4: 31 residues within 4Å:- Chain A: H.101, G.220, I.221, G.222, T.244, Y.245, P.246, 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: TDL.3
24 PLIP interactions:22 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: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:N.286, A:N.286, A:R.315, A:N.417
- Salt bridges: A:H.101
FAD.9: 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, A.420
- Chain D: F.121
- Ligands: TDL.8
25 PLIP interactions:23 interactions with chain B, 2 interactions with chain D- Hydrophobic interactions: 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: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:N.286, B:N.417
- Salt bridges: B:H.101
FAD.14: 31 residues within 4Å:- Chain A: F.121
- Chain C: H.101, G.220, I.221, G.222, T.244, Y.245, P.246, 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: TDL.13
26 PLIP interactions:24 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: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:N.286, C:N.286, C:R.315, C:N.417
- Salt bridges: C:H.101
FAD.19: 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, A.420
- Ligands: TDL.18
26 PLIP interactions:24 interactions with chain D, 2 interactions with chain B- Hydrophobic interactions: 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: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:N.286, D:D.308, D:N.417
- Salt bridges: D:H.101
- 4 x PYR: PYRUVIC ACID(Non-covalent)
PYR.5: 6 residues within 4Å:- Chain A: L.555, R.556, L.557, D.558, M.561, S.562
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:M.561
- Hydrogen bonds: A:L.557, A:D.558
PYR.10: 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.15: 6 residues within 4Å:- Chain C: L.555, R.556, L.557, D.558, M.561, S.562
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:M.561
- Hydrogen bonds: C:L.557, C:D.558
- Water bridges: C:E.272
PYR.20: 6 residues within 4Å:- Chain D: L.555, R.556, L.557, D.558, M.561, S.562
3 PLIP interactions:3 interactions with chain D- Hydrophobic interactions: D:M.561
- Hydrogen bonds: D:L.557, D:D.558
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wille, G. et al., The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Nat.Chem.Biol. (2006)
- Release Date
- 2006-04-25
- Peptides
- Pyruvate oxidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.96 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 4 x TDL: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x PYR: PYRUVIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Wille, G. et al., The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Nat.Chem.Biol. (2006)
- Release Date
- 2006-04-25
- Peptides
- Pyruvate oxidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B