SMTL ID : 2ezu.1

Pyruvate oxidase variant F479W in complex with reaction intermediate 2-acetyl-thiamin diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.447, N.474, Q.476 Ligands: HTL.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:Q.476, H2O.19 MG.7: 5 residues within 4Å: Chain B: D.447, G.448, N.474, Q.476 Ligands: HTL.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:Q.476, H2O.19 MG.11: 4 residues within 4Å: Chain C: D.447, N.474, Q.476 Ligands: HTL.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.447, C:Q.476, H2O.56 MG.17: 5 residues within 4Å: Chain D: D.447, G.448, N.474, Q.476 Ligands: HTL.18 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.447, D:Q.476, H2O.57

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 6 residues within 4Å: Chain A: M.452, Q.455 Chain C: H.58, M.452, Q.455 Ligands: NA.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:Q.455, C: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 B, 1 interactions with chain D Hydrogen bonds: B:M.452, B:Q.455 Water bridges: D:Q.455 NA.12: 6 residues within 4Å: Chain A: H.58, M.452, Q.455 Chain C: M.452, Q.455 Ligands: NA.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Water bridges: A:Q.455, 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:M.452, D:Q.455 Water bridges: B:Q.455

4 x HTL: 2-ACETYL-THIAMINE DIPHOSPHATE(Non-covalent)

HTL.3: 28 residues within 4Å: Chain A: N.92, 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 Chain C: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Ligands: MG.1, FAD.4 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.394, A:M.422, A:Y.477, C:I.32, C:P.85 Hydrogen bonds: A:V.394, A:D.396, A:A.420, A:M.422, A:D.447, A:G.448, A:G.449, A:N.474, A:G.478, A:W.479, C:Q.122 Water bridges: A:G.446, A:G.446, A:G.446, A:D.447, A:D.447 HTL.8: 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, W.479, I.480 Chain D: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Ligands: MG.7, FAD.9 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:V.394, B:Y.477, D:I.32, D:P.85 Hydrogen bonds: B:V.394, B:D.396, B:A.420, B:M.422, B:G.448, B:G.449, B:N.474, B:N.474, B:G.478, B:W.479, D:Q.122 Water bridges: B:I.397, B:G.446, B:G.446, B:G.446, B:D.447, B:D.447, D:E.59 HTL.13: 28 residues within 4Å: Chain A: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Chain C: N.92, 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 Ligands: MG.11, FAD.14 21 PLIP interactions: 3 interactions with chain A, 18 interactions with chain C Hydrophobic interactions: A:I.32, A:P.85, C:V.394, C:M.422, C:Y.477 Hydrogen bonds: A:Q.122, C:V.394, C:D.396, C:A.420, C:M.422, C:G.448, C:G.449, C:N.474, C:G.478, C:W.479 Water bridges: C:D.393, C:G.446, C:G.446, C:G.446, C:D.447, C:D.447 HTL.18: 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, W.479, I.480 Ligands: MG.17, FAD.19 22 PLIP interactions: 19 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:V.394, D:Y.477, B:I.32, B:P.85 Hydrogen bonds: D:V.394, D:D.396, D:D.396, D:A.420, D:M.422, D:G.448, D:G.449, D:N.474, D:N.474, D:G.478, D:W.479, B:Q.122 Water bridges: D:I.397, D:G.446, D:G.446, D:G.446, D:D.447, D:D.447

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

FAD.4: 30 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, N.398, S.416, N.417, A.420 Chain C: F.121 Ligands: HTL.3 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.265, A:A.420, C:F.121, C:F.121 Hydrogen bonds: A:I.221, A:T.244, A:Y.245, A:A.262, A:R.264, A:V.265, A:N.286, A:I.307, A:D.325, A:A.326, A:N.417 Water bridges: A:N.286, A:N.286, A:N.286, A:N.417 Salt bridges: A:H.101 FAD.9: 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, N.398, S.416, N.417, A.420 Chain D: F.121 Ligands: HTL.8 26 PLIP interactions: 24 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.245, B:V.265, 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:D.308, B:R.315, B:N.417 Salt bridges: B:H.101 FAD.14: 30 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, N.398, S.416, N.417, A.420 Ligands: HTL.13 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.265, C:A.420, A:F.121, A:F.121 Hydrogen bonds: C:I.221, C:T.244, C:T.244, C:Y.245, C:A.262, C:R.264, C:V.265, 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:N.286, C:N.417 Salt bridges: C:H.101 FAD.19: 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, N.398, S.416, N.417, A.420 Ligands: HTL.18 27 PLIP interactions: 25 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.245, D:V.265, 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:D.308, D:D.308, D:R.315, 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 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

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
A

B
B

C
A

D
B

Pyruvate oxidase

Related Entries With Identical Sequence