SMTL ID : 2q27.1

Crystal structure of oxalyl-coA decarboxylase from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 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.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:G.476, H2O.1 MG.10: 5 residues within 4Å: Chain B: D.447, S.448, N.474, G.476 Ligands: TPP.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:G.476, H2O.13 MG.18: 4 residues within 4Å: Chain C: D.447, N.474, G.476 Ligands: TPP.24 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.447, C:G.476, H2O.18 MG.27: 5 residues within 4Å: Chain D: D.447, S.448, N.474, G.476 Ligands: TPP.32 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.447, D:G.476, H2O.30

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: M.245, S.246, R.264, L.284, R.403 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: R.501 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: A.263, S.265, F.266, H.351, Q.354, N.355 Ligand excluded by PLIP SO4.5: 8 residues within 4Å: Chain A: G.219, K.220, G.221, G.278, A.279, R.280, T.419 Ligands: SO4.6 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain A: R.158, G.278, A.279, R.280, D.302 Ligands: SO4.5, EDO.8 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: M.245, S.246, R.264, L.284, R.403 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: R.501, K.504 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: A.263, S.265, F.266, H.351, N.355 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain B: R.158, G.219, K.220, G.221, G.278, A.279, R.280, T.419 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain C: M.245, S.246, R.264, L.284, R.403 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain C: R.501 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain C: A.263, S.265, F.266, H.351, Q.354, N.355 Ligand excluded by PLIP SO4.22: 8 residues within 4Å: Chain C: G.219, K.220, G.221, G.278, A.279, R.280, T.419 Ligands: SO4.23 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain C: R.158, G.278, A.279, R.280, D.302 Ligands: SO4.22, EDO.25 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain D: M.245, S.246, R.264, L.284, R.403 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain D: R.501, K.504 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain D: A.263, S.265, F.266, H.351, N.355 Ligand excluded by PLIP SO4.31: 8 residues within 4Å: Chain D: R.158, G.219, K.220, G.221, G.278, A.279, R.280, T.419 Ligand excluded by PLIP

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.7: 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 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:F.452, A:F.452, A:I.477, C:V.77 Hydrogen bonds: A:A.396, A:N.397, A:T.398, A:T.398, A:G.421, A:M.423, A:D.447, A:S.448, A:A.449, A:N.474, A:G.476, A:Y.478 Water bridges: A:T.398, A:T.398 TPP.15: 25 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, G.31, E.54, V.77, P.80, G.81, N.84, E.119 Ligands: MG.10 17 PLIP interactions: 16 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:D.447, B:S.448, B:A.449, B:N.474, B:Y.478 TPP.24: 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.18 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.452, C:F.452, C:I.477, 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:D.447, C:S.448, C:A.449, C:N.474, C:G.476, C:Y.478 TPP.32: 25 residues within 4Å: Chain B: V.30, G.31, 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.27 18 PLIP interactions: 17 interactions with chain D, 1 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

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 6 residues within 4Å: Chain A: G.221, Y.224, S.225, I.303, I.322 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.303 EDO.16: 5 residues within 4Å: Chain B: R.158, G.221, D.302, I.303, I.322 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.303 EDO.25: 6 residues within 4Å: Chain C: G.221, Y.224, S.225, I.303, I.322 Ligands: SO4.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.303 EDO.33: 5 residues within 4Å: Chain D: R.158, G.221, D.302, I.303, I.322 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.303

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

MES.9: 9 residues within 4Å: Chain A: E.549, S.550, G.551 Chain C: G.31, I.32, P.33, V.34, T.35, D.36 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.31, C:T.35, C:D.36, A:E.549 Water bridges: C:M.37 Salt bridges: C:D.36, A:E.549 MES.17: 7 residues within 4Å: Chain B: G.31, I.32, P.33, V.34, T.35, D.36 Chain D: E.549 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:T.35, B:D.36, D:E.549 Water bridges: B:M.37 Salt bridges: B:D.36, D:E.549 MES.26: 9 residues within 4Å: Chain A: G.31, I.32, P.33, V.34, T.35, D.36 Chain C: E.549, S.550, G.551 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.31, A:T.35, A:D.36 Water bridges: A:M.37 Salt bridges: A:D.36, C:E.549 MES.34: 7 residues within 4Å: Chain B: E.549 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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