SMTL ID : 2q29.1

Crystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with acetyl coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 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, G.476 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:G.476, H2O.1 MG.5: 4 residues within 4Å: Chain B: D.447, N.474, G.476 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:G.476, H2O.14 MG.9: 4 residues within 4Å: Chain C: D.447, N.474, G.476 Ligands: TPP.11 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.447, C:G.476, H2O.26 MG.13: 4 residues within 4Å: Chain D: D.447, N.474, G.476 Ligands: TPP.15 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.447, D:G.476, H2O.40

4 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.2: 9 residues within 4Å: Chain A: A.261, A.262, A.263, R.264, S.265, N.355, M.359, R.403, N.404 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.261, A:R.264, A:S.265, A:S.265, A:S.265, A:N.355, A:N.404, A:N.404, A:N.404 Water bridges: A:R.264, A:F.266, A:N.355, A:R.403, A:N.404 Salt bridges: A:R.264, A:R.264, A:R.403, A:R.403 ACO.6: 10 residues within 4Å: Chain B: A.261, A.262, A.263, R.264, S.265, N.355, A.356, M.359, R.403, N.404 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.261, B:R.264, B:S.265, B:S.265, B:S.265, B:N.355, B:N.404, B:N.404, B:N.404 Water bridges: B:R.264, B:R.264, B:F.266, B:R.403, B:N.404 Salt bridges: B:R.264, B:R.264, B:R.403, B:R.403 ACO.10: 9 residues within 4Å: Chain C: A.261, A.262, A.263, R.264, S.265, N.355, M.359, R.403, N.404 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:A.261, C:R.264, C:S.265, C:S.265, C:S.265, C:N.355, C:N.404, C:N.404, C:N.404 Water bridges: C:R.264, C:F.266, C:N.355, C:R.403, C:N.404 Salt bridges: C:R.264, C:R.264, C:R.403, C:R.403 ACO.14: 10 residues within 4Å: Chain D: A.261, A.262, A.263, R.264, S.265, N.355, A.356, M.359, R.403, N.404 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:A.261, D:R.264, D:S.265, D:S.265, D:S.265, D:N.355, D:N.404, D:N.404, D:N.404 Water bridges: D:R.264, D:R.264, D:F.266, D:R.403, D:N.404 Salt bridges: D:R.264, D:R.264, D:R.403, D:R.403

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 23 residues within 4Å: Chain A: Y.372, G.395, A.396, N.397, T.398, G.421, M.423, G.446, D.447, S.448, A.449, F.452, N.474, G.476, I.477, Y.478 Chain C: V.30, E.54, V.77, P.80, G.81, N.84 Ligands: MG.1 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.452, A:F.452, C:V.77 Hydrogen bonds: A:A.396, A:N.397, A:T.398, A:T.398, A:G.421, A:M.423, A:S.448, A:A.449, A:N.474, A:Y.478 Water bridges: A:D.447, A:D.447, C:E.54 TPP.7: 24 residues within 4Å: Chain B: Y.372, G.395, A.396, N.397, T.398, G.421, M.423, G.446, D.447, S.448, A.449, F.452, N.474, G.476, I.477, Y.478 Chain D: V.30, E.54, V.77, P.80, G.81, N.84, E.119 Ligands: MG.5 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.452, B:F.452, B:I.477, D:V.77 Hydrogen bonds: B:A.396, B:N.397, B:T.398, B:T.398, B:T.398, B:G.421, B:M.423, B:D.447, B:S.448, B:A.449, B:N.474, B:Y.478 TPP.11: 23 residues within 4Å: Chain A: V.30, E.54, V.77, P.80, G.81, N.84 Chain C: Y.372, G.395, A.396, N.397, T.398, G.421, M.423, G.446, D.447, S.448, A.449, F.452, N.474, G.476, I.477, Y.478 Ligands: MG.9 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.452, C:F.452, A:V.77 Hydrogen bonds: C:Y.372, C:A.396, C:N.397, C:T.398, C:T.398, C:T.398, C:G.421, C:M.423, C:S.448, C:A.449, C:N.474, C:Y.478 Water bridges: C:D.447, C:D.447 TPP.15: 24 residues within 4Å: Chain B: V.30, E.54, V.77, P.80, G.81, N.84, E.119 Chain D: Y.372, G.395, A.396, N.397, T.398, G.421, M.423, G.446, D.447, S.448, A.449, F.452, N.474, G.476, I.477, Y.478 Ligands: MG.13 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.452, D:F.452, D:I.477, B:V.77 Hydrogen bonds: D:Y.372, D:A.396, D:N.397, D:T.398, D:T.398, D:G.421, D:M.423, D:D.447, D:S.448, D:A.449, D:N.474, D:Y.478 Water bridges: D:T.398, D:T.398, B:E.54

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 8 residues within 4Å: Chain A: G.31, I.32, P.33, V.34, T.35, D.36 Chain C: E.549, S.550 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.35, A:T.35, A:D.36 Water bridges: A:T.35, A:M.37 Salt bridges: A:D.36, C:E.549 MES.8: 8 residues within 4Å: Chain B: G.31, I.32, P.33, V.34, T.35, D.36 Chain D: E.549, S.550 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:E.549, B:T.35, B:D.36 Salt bridges: D:E.549, B:D.36 Water bridges: B:T.35, B:M.37 MES.12: 8 residues within 4Å: Chain A: E.549, S.550 Chain C: G.31, I.32, P.33, V.34, T.35, D.36 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Water bridges: A:E.549, C:M.37 Salt bridges: A:E.549, C:D.36 Hydrogen bonds: C:T.35, C:T.35, C:T.35, C:D.36 MES.16: 8 residues within 4Å: Chain B: E.549, S.550 Chain D: G.31, I.32, P.33, V.34, T.35, D.36 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:T.35, D:T.35, D:D.36 Water bridges: D:M.37 Salt bridges: D:D.36, B:E.549

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Werther, T. et al., New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli. Febs J. (2010)

Release Date

2008-06-03

Peptides

oxalyl-CoA decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

oxalyl-CoA decarboxylase

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