SMTL ID : 2c31.1

CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE COFACTOR DERIVATIVE THIAMIN-2-THIAZOLONE DIPHOSPHATE AND ADENOSINE DIPHOSPHATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.452, N.479, G.481 Ligands: TZD.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.452, A:G.481, H2O.14 MG.4: 4 residues within 4Å: Chain B: D.452, N.479, G.481 Ligands: TZD.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.452, B:G.481, H2O.24 MG.7: 4 residues within 4Å: Chain C: D.452, N.479, G.481 Ligands: TZD.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.452, C:G.481, H2O.39 MG.10: 4 residues within 4Å: Chain D: D.452, N.479, G.481 Ligands: TZD.11 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.452, D:G.481, H2O.50

4 x TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TZD.2: 26 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, G.33, E.56, V.79, P.82, G.83, N.86, Y.120, E.121 Ligands: MG.1 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.457, A:I.482, B:V.79, B:P.82 Hydrogen bonds: A:A.401, A:N.402, A:N.402, A:A.403, A:G.426, A:M.428, A:S.453, A:S.453, A:A.454, A:G.481, A:Y.483, B:Y.120 Water bridges: A:D.452, A:D.452, B:I.34, B:E.56 TZD.5: 26 residues within 4Å: Chain A: V.32, G.33, E.56, V.79, P.82, G.83, N.86, Y.120, 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.4 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.457, B:I.482, A:V.79 Hydrogen bonds: B:A.401, B:N.402, B:N.402, B:A.403, B:G.426, B:M.428, B:D.452, B:S.453, B:S.453, B:A.454, B:Y.483, A:Y.120 Water bridges: A:I.34 TZD.8: 26 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, G.33, E.56, V.79, P.82, G.83, N.86, Y.120, E.121 Ligands: MG.7 21 PLIP interactions: 17 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.457, C:I.482, D:V.79, D:P.82 Hydrogen bonds: C:Y.377, C:A.401, C:N.402, C:N.402, C:A.403, C:G.426, C:M.428, C:S.453, C:S.453, C:A.454, C:N.479, C:G.481, C:Y.483 Water bridges: C:D.452, C:D.452, D:I.34, D:Y.120 TZD.11: 26 residues within 4Å: Chain C: V.32, G.33, E.56, V.79, P.82, G.83, N.86, Y.120, 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.10 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.457, D:I.482, C:V.79 Hydrogen bonds: D:Y.377, 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:S.453, D:A.454, D:N.479, D:Y.483, C:Y.120 Water bridges: C:I.34

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

ADP.3: 18 residues within 4Å: Chain A: C.98, R.160, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, G.324, D.325, I.326, T.424 15 PLIP interactions: 15 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 Water bridges: A:A.250, A:R.282, A:R.282, A:T.424 Salt bridges: A:K.222, A:K.222, A:R.282 ADP.6: 20 residues within 4Å: Chain B: 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, G.324, D.325, I.326, T.424 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.160, B:R.160, B:K.222, B:R.282, B:N.284, B:I.307, B:I.326 Water bridges: B:K.222, B:K.222, B:N.284, B:N.284, B:K.327 Salt bridges: B:K.222, B:K.222, B:R.282 ADP.9: 18 residues within 4Å: Chain C: C.98, R.160, G.221, K.222, G.223, Y.226, M.247, G.280, A.281, R.282, N.284, L.286, D.306, I.307, G.324, D.325, I.326, T.424 15 PLIP interactions: 15 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:A.250, C:R.282, C:R.282 Salt bridges: C:K.222, C:K.222, C:R.282 ADP.12: 20 residues within 4Å: Chain D: 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, G.324, D.325, I.326, T.424 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:R.160, D:R.160, D:K.222, D:R.282, D:N.284, D:I.307, D:I.326, D:T.424 Water bridges: D:K.222, D:K.222, D:N.284, D:N.284, D:D.325 Salt bridges: D:K.222, D:K.222, D:R.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berthold, C.L. et al., Structural Basis for Activation of the Thiamin Diphosphate-Dependent Enzyme Oxalyl-Coa Decarboxylase by Adenosine Diphosphate. J.Biol.Chem. (2005)

Release Date

2005-10-07

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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