SMTL ID : 2ez4.1

Pyruvate oxidase variant F479W

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 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: TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:Q.476, H2O.19 MG.7: 4 residues within 4Å: Chain B: D.447, N.474, Q.476 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:Q.476, H2O.37 MG.11: 4 residues within 4Å: Chain C: D.447, N.474, Q.476 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.447, C:Q.476, H2O.56 MG.17: 4 residues within 4Å: Chain D: D.447, N.474, Q.476 Ligands: TPP.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.447, D:Q.476, H2O.75

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 7 residues within 4Å: Chain A: G.34, G.35, F.121, Q.122 Chain C: W.479, I.480, E.483 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.35 Water bridges: A:S.36, A:S.36, C:R.264, C:W.479, C:E.483 PO4.8: 7 residues within 4Å: Chain B: W.479, I.480, E.483 Chain D: G.34, G.35, F.121, Q.122 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:G.35, B:E.483, B:E.483 Water bridges: D:S.36, D:S.36, B:R.264 PO4.12: 7 residues within 4Å: Chain A: W.479, I.480, E.483 Chain C: G.34, G.35, F.121, Q.122 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.35 Water bridges: C:S.36, C:S.36, A:R.264, A:W.479, A:E.483 PO4.18: 7 residues within 4Å: Chain B: G.34, G.35, F.121, Q.122 Chain D: W.479, I.480, E.483 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:E.483, D:E.483, B:G.35 Water bridges: D:R.264, B:S.36, B:S.36

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

NA.3: 5 residues within 4Å: Chain A: M.452, Q.455 Chain C: M.452, Q.455 Ligands: NA.13 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:M.452, C:Q.455, A:Q.455 NA.6: 6 residues within 4Å: Chain B: M.452, Q.455 Chain D: H.58, 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 Water bridges: D:Q.455, B:Q.455 NA.13: 5 residues within 4Å: Chain A: M.452, Q.455 Chain C: M.452, Q.455 Ligands: NA.3 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:M.452, C:Q.455, A:Q.455 NA.16: 6 residues within 4Å: Chain B: H.58, M.452, Q.455 Chain D: M.452, Q.455 Ligands: NA.6 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Water bridges: D:Q.455, B:Q.455 Hydrogen bonds: B:M.452

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 26 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 Chain C: I.32, P.33, E.59, S.82, P.85, G.86, H.89, Q.122 Ligands: MG.1 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:Y.477, C:I.32, C:P.85 Hydrogen bonds: A:D.396, A:A.420, A:M.422, A:G.448, A:G.449, A:N.474, A:G.478, A:W.479, C:Q.122 Water bridges: A:I.397, A:I.397, A:G.446, A:G.446, A:D.447, A:D.447 TPP.9: 25 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 21 PLIP interactions: 5 interactions with chain D, 16 interactions with chain B Hydrophobic interactions: D:I.32, D:P.85, B:Y.477 Hydrogen bonds: D:S.82, D:Q.122, B:D.396, B:A.420, B:M.422, B:G.448, B:G.449, B:N.474, B:Q.476, B:G.478, B:W.479 Water bridges: D:E.59, B:I.397, B:I.397, B:G.446, B:G.446, B:D.447, B:D.447 TPP.14: 26 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, 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 20 PLIP interactions: 4 interactions with chain A, 16 interactions with chain C Hydrophobic interactions: A:I.32, A:P.85, C:Y.477 Hydrogen bonds: A:Q.122, C:D.396, 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: A:E.59, C:I.397, C:I.397, C:G.446, C:G.446, C:D.447, C:D.447 TPP.19: 25 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 21 PLIP interactions: 4 interactions with chain B, 17 interactions with chain D Hydrophobic interactions: B:I.32, B:P.85, D:Y.477 Hydrogen bonds: B:S.82, B:Q.122, D:D.396, D:D.396, D:A.420, D:M.422, D:G.448, D:G.449, D:N.474, D:Q.476, D:G.478, D:W.479 Water bridges: D:I.397, D:I.397, D:G.446, D:G.446, D:D.447, D:D.447

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

FAD.5: 31 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 23 PLIP interactions: 21 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:N.417 Salt bridges: A:H.101 FAD.10: 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, V.394, N.398, S.416, N.417, A.420 Chain D: F.121 26 PLIP interactions: 24 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:R.224, B:A.262, B:N.286, B:N.286, B:N.286, B:N.417 Salt bridges: B:H.101 FAD.15: 31 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 26 PLIP interactions: 2 interactions with chain A, 24 interactions with chain C Hydrophobic interactions: A:F.121, A:F.121, C:Y.245, C:V.265, C:V.394, C:A.420 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:N.286, C:N.417 Salt bridges: C:H.101 FAD.20: 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, V.394, N.398, S.416, N.417, A.420 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:R.224, D:A.262, D:N.286, D:N.286, D:N.286, 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
A

B
B

C
A

D
B

Pyruvate oxidase

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