SMTL ID : 2ji6.1

X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP and oxalyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-tetramer

Ligands

4 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TPW.1: 25 residues within 4Å: Chain A: Y.377, G.400, A.401, N.402, A.403, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483 Chain B: V.32, E.56, V.79, P.82, G.83, N.86, E.121 Ligands: MG.2, OXK.4 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.457, A:I.482, B:V.79, B:P.82 Hydrogen bonds: A:Y.377, A:A.401, A:N.402, A:N.402, A:A.403, A:G.426, A:M.428, A:D.452, A:S.453, A:S.453, A:A.454, A:N.479, A:Y.483 TPW.7: 27 residues within 4Å: Chain A: V.31, V.32, G.33, E.56, V.79, P.82, G.83, N.86, E.121 Chain B: Y.377, G.400, A.401, N.402, A.403, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483 Ligands: MG.8, OXK.10 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.457, B:I.482, A:V.31, A:V.79, A:P.82 Hydrogen bonds: B:Y.377, B:A.401, B:N.402, B:N.402, B:A.403, B:G.426, B:M.428, B:S.453, B:A.454, B:N.479, B:Y.483 Water bridges: B:D.452, B:D.452 TPW.13: 25 residues within 4Å: Chain C: Y.377, G.400, A.401, N.402, A.403, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483 Chain D: V.32, E.56, V.79, P.82, G.83, N.86, E.121 Ligands: MG.14, OXK.16 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.457, C:I.482, D:V.79, D:P.82 Hydrogen bonds: C:A.401, C:N.402, C:N.402, C:A.403, C:G.426, C:M.428, C:D.452, C:D.452, C:S.453, C:S.453, C:A.454, C:N.479, C:Y.483 TPW.19: 27 residues within 4Å: Chain C: V.31, V.32, G.33, E.56, V.79, P.82, G.83, N.86, E.121 Chain D: Y.377, G.400, A.401, N.402, A.403, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483 Ligands: MG.20, OXK.22 18 PLIP interactions: 3 interactions with chain C, 15 interactions with chain D Hydrophobic interactions: C:V.31, C:V.79, C:P.82, D:F.457, D:I.482 Hydrogen bonds: D:A.401, D:N.402, D:N.402, D:A.403, D:G.426, D:M.428, D:D.452, D:S.453, D:A.454, D:N.479, D:Y.483 Water bridges: D:D.452, D:D.452

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.452, N.479, G.481 Ligands: TPW.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.452, A:G.481, H2O.15 MG.8: 4 residues within 4Å: Chain B: D.452, N.479, G.481 Ligands: TPW.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.452, B:G.481, H2O.35 MG.14: 4 residues within 4Å: Chain C: D.452, N.479, G.481 Ligands: TPW.13 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.452, C:G.481, H2O.50 MG.20: 4 residues within 4Å: Chain D: D.452, N.479, G.481 Ligands: TPW.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.452, D:G.481, H2O.70

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

ADP.3: 22 residues within 4Å: Chain A: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, A.227, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, Q.308, G.324, D.325, I.326, T.424 Ligands: PGE.5 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.160, A:R.160, A:K.222, A:R.282, A:R.282, A:N.284, A:I.307, A:I.326, A:T.424, A:T.424 Water bridges: A:K.222, A:R.282, A:D.325 Salt bridges: A:K.222, A:K.222, A:R.282 ADP.9: 18 residues within 4Å: Chain B: C.98, R.160, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, L.286, D.306, I.307, G.324, D.325, I.326, T.424 Ligands: PGE.11 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.160, B:R.160, B:K.222, B:R.282, B:R.282, B:N.284, B:I.307, B:I.326, B:T.424, B:T.424 Water bridges: B:K.222, B:R.282, B:D.325, B:D.325 Salt bridges: B:K.222, B:K.222, B:R.282 ADP.15: 22 residues within 4Å: Chain C: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, A.227, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, Q.308, G.324, D.325, I.326, T.424 Ligands: PGE.17 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:R.160, C:R.160, C:K.222, C:R.282, C:R.282, C:N.284, C:I.307, C:I.326, C:T.424 Water bridges: C:K.222, C:R.282, C:K.327, C:T.424 Salt bridges: C:K.222, C:K.222, C:R.282 ADP.21: 18 residues within 4Å: Chain D: C.98, R.160, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, L.286, D.306, I.307, G.324, D.325, I.326, T.424 Ligands: PGE.23 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:R.160, D:R.160, D:K.222, D:R.282, D:R.282, D:N.284, D:I.307, D:I.326, D:T.424 Water bridges: D:K.222, D:R.282, D:D.325, D:K.327, D:T.424 Salt bridges: D:K.222, D:K.222, D:R.282

4 x OXK: OXALYL-COENZYME A(Non-covalent)

OXK.4: 27 residues within 4Å: Chain A: A.263, A.264, T.265, R.266, A.267, W.285, L.286, Q.288, N.358, K.359, L.362, G.400, L.404, D.405, R.408, M.409, G.426, M.428, Y.483, S.553, R.555, I.556 Chain B: G.33, I.34, Y.120, E.121 Ligands: TPW.1 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.404, A:I.556 Hydrogen bonds: A:A.263, A:R.266, A:A.267, A:R.408, A:R.408, A:M.409, B:I.34, B:Y.120, B:Y.120 Water bridges: A:R.266, A:F.268, A:A.401, A:D.405, A:G.426, A:R.555, A:R.555, A:R.555, B:E.121 Salt bridges: A:R.266, A:R.408, A:R.555, A:R.555, A:R.555 OXK.10: 25 residues within 4Å: Chain A: G.33, I.34, Y.120 Chain B: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, G.400, L.404, D.405, R.408, M.409, G.426, M.428, Y.483, S.553, R.555, I.556 Ligands: TPW.7 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.286, B:L.404 Hydrogen bonds: B:A.264, B:R.266, B:A.267, B:R.408, B:R.408, B:M.409, A:I.34, A:Y.120 Water bridges: B:R.266, B:R.266, B:K.359, B:A.401, B:D.405, A:E.121 Salt bridges: B:R.266, B:R.408, B:R.555, B:R.555 OXK.16: 27 residues within 4Å: Chain C: A.263, A.264, T.265, R.266, A.267, W.285, L.286, Q.288, N.358, K.359, L.362, G.400, L.404, D.405, R.408, M.409, G.426, M.428, Y.483, S.553, R.555, I.556 Chain D: G.33, I.34, Y.120, E.121 Ligands: TPW.13 25 PLIP interactions: 22 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.404, C:I.556 Hydrogen bonds: C:A.263, C:R.266, C:A.267, C:R.408, C:R.408, C:M.409, C:Y.483, D:I.34, D:Y.120, D:Y.120 Water bridges: C:R.266, C:F.268, C:A.401, C:D.405, C:G.426, C:R.555, C:R.555, C:R.555 Salt bridges: C:R.266, C:R.408, C:R.555, C:R.555, C:R.555 OXK.22: 25 residues within 4Å: Chain C: G.33, I.34, Y.120 Chain D: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, G.400, L.404, D.405, R.408, M.409, G.426, M.428, Y.483, S.553, R.555, I.556 Ligands: TPW.19 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.286, D:L.404 Hydrogen bonds: D:A.264, D:R.266, D:A.267, D:R.408, D:R.408, D:M.409, D:Y.483, C:I.34, C:Y.120 Water bridges: D:R.266, D:R.266, D:K.359, D:A.401, D:D.405 Salt bridges: D:R.266, D:R.408, D:R.555, D:R.555

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 9 residues within 4Å: Chain A: E.70, G.71, A.193, P.194, Y.226, A.227, Q.228, D.325 Ligands: ADP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.70, A:D.325 Water bridges: A:Q.228 PGE.11: 9 residues within 4Å: Chain B: E.70, G.71, A.193, P.194, A.195, Y.226, A.227, D.325 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.193 PGE.17: 9 residues within 4Å: Chain C: E.70, G.71, A.193, P.194, Y.226, A.227, Q.228, D.325 Ligands: ADP.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.70, C:D.325 Water bridges: C:Q.228 PGE.23: 9 residues within 4Å: Chain D: E.70, G.71, A.193, P.194, A.195, Y.226, A.227, D.325 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain D Water bridges: D:A.193

4 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.6: 7 residues within 4Å: Chain A: D.489, G.493, V.494, I.495, R.499 Chain B: N.469, K.537 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.493, A:R.499, A:R.499, B:N.469, B:K.537, B:K.537 Water bridges: A:G.493, A:S.496 B3P.12: 6 residues within 4Å: Chain A: N.469, K.537 Chain B: D.489, G.493, V.494, R.499 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.537, A:K.537, B:G.493, B:R.499, B:R.499 Water bridges: B:D.489 B3P.18: 7 residues within 4Å: Chain C: D.489, G.493, V.494, I.495, R.499 Chain D: N.469, K.537 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.493, C:R.499, C:R.499, D:N.469, D:K.537, D:K.537 Water bridges: C:G.493, C:S.496 B3P.24: 6 residues within 4Å: Chain C: N.469, K.537 Chain D: D.489, G.493, V.494, R.499 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.537, C:K.537, D:G.493, D:R.499, D:R.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berthold, C.L. et al., Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases. Structure (2007)

Release Date

2007-07-17

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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