- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 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.10
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:M.452, C:Q.455
- Water bridges: A:Q.455
NA.5: 5 residues within 4Å:- Chain B: M.452, Q.455
- Chain D: M.452, Q.455
- Ligands: NA.13
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.10: 5 residues within 4Å:- Chain A: M.452, Q.455
- Chain C: M.452, Q.455
- Ligands: NA.2
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:M.452, A:Q.455
- Water bridges: C:Q.455
NA.13: 5 residues within 4Å:- Chain B: M.452, Q.455
- Chain D: M.452, Q.455
- Ligands: NA.5
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain B- Hydrogen bonds: D:Q.455, B:Q.455, B:Q.455
- 4 x TDK: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)
TDK.3: 31 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, 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.111, F.121, Q.122
- Ligands: MG.1, FAD.4
24 PLIP interactions:18 interactions with chain A, 6 interactions with chain C- Hydrophobic interactions: A:V.394, A:Y.477, C:I.32, C:P.85
- Hydrogen bonds: A:D.396, A:D.396, A:A.420, A:A.420, A:M.422, A:G.446, A:D.447, A:G.448, A:G.449, A:N.474, A:G.478, A:W.479, A:W.479, C:G.35, C:Q.122
- Water bridges: A:I.397, A:I.397, A:G.446, C:S.36, C:S.36
TDK.7: 31 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.111, F.121, Q.122
- Ligands: MG.6, FAD.8
27 PLIP interactions:21 interactions with chain B, 6 interactions with chain D- Hydrophobic interactions: B:V.394, B:Y.477, D:I.32, D:P.85
- Hydrogen bonds: B:D.396, B:D.396, B:A.420, B:A.420, B:M.422, B:G.446, B:D.447, B:G.448, B:G.449, B:N.474, B:G.478, B:W.479, B:W.479, D:G.35, D:Q.122
- Water bridges: B:D.393, B:I.397, B:I.397, B:G.446, B:D.447, B:D.447, D:S.36, D:E.59
TDK.11: 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.111, F.121, 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, W.479, I.480, E.483
- Ligands: MG.9, FAD.12
27 PLIP interactions:7 interactions with chain A, 20 interactions with chain C- Hydrophobic interactions: A:I.32, A:P.85, C:V.394, C:Y.477
- Hydrogen bonds: A:G.35, A:Q.122, C:D.396, C:D.396, C:D.396, C:A.420, C:A.420, C:M.422, C:G.446, C:D.447, C:G.448, C:G.449, C:N.474, C:G.478, C:W.479, C:W.479
- Water bridges: A:S.36, A:S.36, A:E.59, C:D.393, C:I.397, C:I.397, C:G.446
TDK.15: 31 residues within 4Å:- Chain B: I.32, P.33, G.34, G.35, E.59, S.82, P.85, G.86, H.89, F.111, 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.14, FAD.16
25 PLIP interactions:20 interactions with chain D, 5 interactions with chain B- Hydrophobic interactions: D:V.394, D:Y.477, B:I.32, B:P.85
- Hydrogen bonds: D:D.396, D:D.396, D:D.396, D:A.420, 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:Q.122
- Water bridges: D:I.397, D:I.397, 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: TDK.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.8: 31 residues within 4Å:- Chain B: 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 D: F.121
- Ligands: TDK.7
24 PLIP interactions:22 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:N.286, B:N.286, B:R.315, B:N.417
- Salt bridges: B:H.101
FAD.12: 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: TDK.11
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.16: 31 residues within 4Å:- Chain B: F.121
- Chain D: 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: TDK.15
24 PLIP interactions:22 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: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
- 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 1.60 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 4 x TDK: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)
- 4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(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