SMTL ID : 2q28.1

Crystal structure of oxalyl-coA decarboxylase from Escherichia coli in complex with adenosine-5`-diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 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.3 MG.8: 4 residues within 4Å: Chain B: D.447, N.474, G.476 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:G.476, H2O.22 MG.15: 4 residues within 4Å: Chain C: D.447, N.474, G.476 Ligands: TPP.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.447, C:G.476, H2O.37 MG.22: 4 residues within 4Å: Chain D: D.447, N.474, G.476 Ligands: TPP.24 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.447, D:G.476, H2O.56

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

SO4.2: 5 residues within 4Å: Chain A: Y.118 Chain C: A.396, Y.478, S.550 Ligands: TPP.17 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.550, A:Y.118 Water bridges: A:Y.118 SO4.9: 6 residues within 4Å: Chain B: I.32, Y.118 Chain D: A.396, Y.478, S.550 Ligands: TPP.24 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.118, D:S.550 Water bridges: B:Y.118, B:Y.118 SO4.16: 5 residues within 4Å: Chain A: A.396, Y.478, S.550 Chain C: Y.118 Ligands: TPP.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.478, A:S.550, C:Y.118, C:Y.118 SO4.23: 6 residues within 4Å: Chain B: A.396, Y.478, S.550 Chain D: I.32, Y.118 Ligands: TPP.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.478, B:S.550, D:Y.118, D:Y.118

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 25 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, E.119 Ligands: MG.1, SO4.16 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.452, A:F.452, A:I.477, C:V.77, C:P.80 Hydrogen bonds: A:Y.372, A:A.396, A:N.397, A:T.398, A:T.398, A:T.398, A:G.421, A:M.423, A:S.448, A:A.449, A:N.474, A:G.476, A:Y.478 Water bridges: A:D.447, A:D.447 TPP.10: 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, E.54, V.77, P.80, G.81, N.84, E.119 Ligands: MG.8, SO4.23 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.452, B:F.452, B:I.477, D:V.77 Hydrogen bonds: B:Y.372, B:A.396, B:N.397, 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 Water bridges: B:T.398, B:T.398, D:E.54 TPP.17: 25 residues within 4Å: Chain A: V.30, E.54, V.77, P.80, G.81, N.84, E.119 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: SO4.2, MG.15 20 PLIP interactions: 3 interactions with chain A, 17 interactions with chain C Hydrophobic interactions: A:V.77, A:P.80, C:F.452, C:F.452, C:I.477 Water bridges: A:E.54, C:D.447, C:D.447 Hydrogen bonds: C:A.396, C:N.397, 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.24: 25 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: SO4.9, MG.22 16 PLIP interactions: 15 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:A.396, D:N.397, D:T.398, 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

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 22 residues within 4Å: Chain A: N.95, R.158, P.159, G.219, K.220, G.221, Y.224, S.225, M.245, G.278, A.279, R.280, N.282, L.284, D.302, I.303, E.304, G.320, D.321, I.322, T.419 Ligands: EDO.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.158, A:R.158, A:K.220, A:R.280, A:N.282, A:I.303, A:I.322, A:T.419 Water bridges: A:R.280, A:R.280, A:A.323 Salt bridges: A:K.220, A:K.220, A:R.280 ADP.11: 22 residues within 4Å: Chain B: N.95, R.158, P.159, G.219, K.220, G.221, Y.224, S.225, M.245, G.278, A.279, R.280, N.282, L.284, D.302, I.303, E.304, G.320, D.321, I.322, T.419 Ligands: EDO.13 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.158, B:R.158, B:K.220, B:R.280, B:N.282, B:I.303, B:I.322, B:T.419, B:T.419 Water bridges: B:R.280, B:R.280, B:D.321 Salt bridges: B:K.220, B:K.220, B:R.280 ADP.18: 22 residues within 4Å: Chain C: N.95, R.158, P.159, G.219, K.220, G.221, Y.224, S.225, M.245, G.278, A.279, R.280, N.282, L.284, D.302, I.303, E.304, G.320, D.321, I.322, T.419 Ligands: EDO.20 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:R.158, C:R.158, C:K.220, C:R.280, C:N.282, C:I.303, C:I.322 Water bridges: C:R.280, C:R.280, C:D.321, C:T.419 Salt bridges: C:K.220, C:K.220, C:R.280 ADP.25: 22 residues within 4Å: Chain D: N.95, R.158, P.159, G.219, K.220, G.221, Y.224, S.225, M.245, G.278, A.279, R.280, N.282, L.284, D.302, I.303, E.304, G.320, D.321, I.322, T.419 Ligands: EDO.27 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.158, D:R.158, D:K.220, D:R.280, D:N.282, D:I.303, D:I.322, D:T.419 Water bridges: D:R.280, D:R.280, D:A.323 Salt bridges: D:K.220, D:K.220, D:R.280

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

MES.5: 11 residues within 4Å: Chain A: E.549, S.550, G.551, H.552, I.553 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:T.35, C:D.36, C:D.36 Water bridges: C:T.35, C:M.37, A:H.552, A:H.552 MES.12: 11 residues within 4Å: Chain B: E.549, S.550, G.551, H.552, I.553 Chain D: G.31, I.32, P.33, V.34, T.35, D.36 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:T.35, D:D.36, D:D.36, B:E.549 Water bridges: D:T.35, D:M.37, B:H.552 Salt bridges: D:D.36, B:E.549 MES.19: 11 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, H.552, I.553 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.35, A:T.35, A:D.36, A:D.36 Water bridges: A:M.37, C:H.552, C:H.552 MES.26: 11 residues within 4Å: Chain B: G.31, I.32, P.33, V.34, T.35, D.36 Chain D: E.549, S.550, G.551, H.552, I.553 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:T.35, B:T.35, B:D.36, B:D.36 Water bridges: B:M.37, D:H.552 Salt bridges: B:D.36, D:E.549

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

EDO.6: 8 residues within 4Å: Chain A: N.95, G.96, F.97, P.159, K.220, G.221, Y.224 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) EDO.7: 5 residues within 4Å: Chain A: H.287, K.289, N.311 Chain C: I.110, Q.115 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Water bridges: A:K.289, A:K.289, A:N.311, A:R.312, A:R.312, C:Q.115, C:Q.115 EDO.13: 8 residues within 4Å: Chain B: N.95, G.96, F.97, P.159, K.220, G.221, Y.224 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: P.313 Chain B: I.145, T.182, T.183, V.185 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:T.182, B:T.183, A:R.312, A:R.312, A:R.312, A:R.312 EDO.20: 8 residues within 4Å: Chain C: N.95, G.96, F.97, P.159, K.220, G.221, Y.224 Ligands: ADP.18 No protein-ligand interaction detected (PLIP) EDO.21: 5 residues within 4Å: Chain A: I.110, Q.115 Chain C: H.287, K.289, N.311 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Water bridges: C:K.289, C:K.289, C:N.311, C:R.312, C:R.312, A:Q.115, A:Q.115 EDO.27: 8 residues within 4Å: Chain D: N.95, G.96, F.97, P.159, K.220, G.221, Y.224 Ligands: ADP.25 No protein-ligand interaction detected (PLIP) EDO.28: 5 residues within 4Å: Chain C: P.313 Chain D: I.145, T.182, T.183, V.185 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Water bridges: D:T.182, D:T.183, C:R.312, C:R.312, C:R.312, C:R.312

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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