SMTL ID : 2ji7.1

X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

4 x OXT: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1R,11R,15S,17R)-19-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-1,11,15,17-TETRAHYDROXY-12,12-DIMETHYL-15,17-DIOXIDO-6,10-DIOXO-14,16,18-TRIOXA-2-THIA-5,9-DIAZA-15,17-DIPHOSPHANONADEC-1-YL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)

OXT.1: 42 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, Y.377, G.400, A.401, N.402, A.403, L.404, D.405, R.408, M.409, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483, R.555, I.556 Chain B: V.32, E.56, V.79, P.82, G.83, N.86, Y.120, E.121 Ligands: MG.2 36 PLIP interactions: 30 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.457, A:I.556, B:V.79, B:P.82 Hydrogen bonds: A:R.266, A:A.267, A:Y.377, A:A.401, A:N.402, A:N.402, A:A.403, A:R.408, A:R.408, A:M.409, A:G.426, A:M.428, A:D.452, A:S.453, A:A.454, A:N.479, A:Y.483, B:Y.120 Water bridges: A:T.265, A:F.268, A:A.401, A:D.405, A:R.555, A:R.555, B:Y.120, B:Y.120, B:E.121 Salt bridges: A:R.266, A:R.408, A:R.555, A:R.555, A:R.555 OXT.8: 41 residues within 4Å: Chain A: V.32, E.56, V.79, P.82, G.83, N.86, Y.120, E.121 Chain B: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, Y.377, G.400, A.401, N.402, A.403, L.404, D.405, R.408, M.409, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483, R.555, I.556 Ligands: MG.9 43 PLIP interactions: 37 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.285, B:W.285, B:F.457, B:I.556, A:V.79, A:P.82 Hydrogen bonds: B:R.266, B:A.267, B:Y.377, B:A.401, B:N.402, B:N.402, B:A.403, B:R.408, B:R.408, B:M.409, B:G.426, B:M.428, B:D.452, B:S.453, B:S.453, B:A.454, B:N.479, B:Y.483, A:Y.120 Water bridges: B:T.265, B:F.268, B:R.385, B:A.401, B:D.405, B:D.405, B:R.555, B:R.555, B:R.555, B:R.555, A:I.34, A:Y.120, A:E.121 Salt bridges: B:R.266, B:R.408, B:R.555, B:R.555, B:R.555 OXT.15: 42 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, Y.377, G.400, A.401, N.402, A.403, L.404, D.405, R.408, M.409, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483, R.555, I.556 Chain D: V.32, E.56, V.79, P.82, G.83, N.86, Y.120, E.121 Ligands: MG.16 35 PLIP interactions: 31 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.457, C:I.556, D:V.79, D:P.82 Hydrogen bonds: C:R.266, C:A.267, C:A.401, C:N.402, C:N.402, C:A.403, C:R.408, C:R.408, C:M.409, C:G.426, C:M.428, C:D.452, C:D.452, C:S.453, C:A.454, C:N.479, C:G.481, C:Y.483, D:Y.120, D:Y.120 Water bridges: C:T.265, C:F.268, C:A.401, C:D.405, C:R.555, C:R.555 Salt bridges: C:R.266, C:R.408, C:R.555, C:R.555, C:R.555 OXT.22: 41 residues within 4Å: Chain C: V.32, E.56, V.79, P.82, G.83, N.86, Y.120, E.121 Chain D: A.263, A.264, T.265, R.266, A.267, W.285, L.286, N.358, K.359, L.362, Y.377, G.400, A.401, N.402, A.403, L.404, D.405, R.408, M.409, G.426, M.428, G.451, D.452, S.453, A.454, F.457, N.479, G.481, I.482, Y.483, R.555, I.556 Ligands: MG.23 41 PLIP interactions: 36 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:W.285, D:W.285, D:F.457, D:I.556, C:V.79, C:P.82 Hydrogen bonds: D:R.266, D:A.267, D:A.401, D:N.402, D:N.402, D:A.403, D:R.408, D:R.408, D:M.409, D:G.426, D:M.428, D:D.452, D:D.452, D:S.453, D:S.453, D:A.454, D:Y.483, C:Y.120, C:Y.120 Water bridges: D:T.265, D:F.268, D:R.385, D:A.401, D:D.405, D:D.405, D:R.555, D:R.555, D:R.555, D:R.555, C:I.34 Salt bridges: D:R.266, D:R.408, D:R.555, D:R.555, D:R.555

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.452, N.479, G.481 Ligands: OXT.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.452, A:G.481, H2O.19 MG.9: 4 residues within 4Å: Chain B: D.452, N.479, G.481 Ligands: OXT.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.452, B:G.481, H2O.42 MG.16: 4 residues within 4Å: Chain C: D.452, N.479, G.481 Ligands: OXT.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.452, C:G.481, H2O.64 MG.23: 4 residues within 4Å: Chain D: D.452, N.479, G.481 Ligands: OXT.22 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.452, D:G.481, H2O.87

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

ADP.3: 20 residues within 4Å: Chain A: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, 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 17 PLIP interactions: 17 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:A.250, A:R.282, A:R.282, A:D.325 Salt bridges: A:K.222, A:K.222, A:R.282 ADP.10: 21 residues within 4Å: Chain B: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, 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.11 16 PLIP interactions: 16 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, B:T.424, B:T.424 Water bridges: B:A.250, B:R.282, B:R.282, B:D.325 Salt bridges: B:K.222, B:K.222, B:R.282 ADP.17: 20 residues within 4Å: Chain C: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, 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 17 PLIP interactions: 17 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, C:K.327, C:T.424 Salt bridges: C:K.222, C:K.222, C:R.282 ADP.24: 21 residues within 4Å: Chain D: C.98, R.160, P.161, G.221, K.222, G.223, Y.226, 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.25 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:A.250, D:R.282, D:R.282, D:K.327, D:T.424 Salt bridges: D:K.222, D:K.222, D:R.282

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

PGE.4: 8 residues within 4Å: Chain A: E.70, G.71, A.193, P.194, Y.226, A.227, Q.228, D.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.194 Water bridges: A:Y.226, A:Y.226, A:D.325 PGE.11: 10 residues within 4Å: Chain B: E.70, G.71, A.193, P.194, A.195, Y.226, A.227, Q.228, D.325 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.194 Water bridges: B:Y.226 PGE.18: 8 residues within 4Å: Chain C: E.70, G.71, A.193, P.194, Y.226, A.227, Q.228, D.325 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.194 PGE.25: 10 residues within 4Å: Chain D: E.70, G.71, A.193, P.194, A.195, Y.226, A.227, Q.228, D.325 Ligands: ADP.24 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.194

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

B3P.5: 7 residues within 4Å: Chain A: D.489, G.493, V.494, I.495, R.499 Chain B: N.469, K.537 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.493, A:R.499, B:N.469, B:K.537 Water bridges: A:D.489, A:S.496 B3P.6: 6 residues within 4Å: Chain A: M.366, T.367, G.382, V.383, R.385, D.386 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.367, A:T.367, A:G.382, A:R.385, A:D.386, A:D.386 Water bridges: A:D.386 B3P.7: 6 residues within 4Å: Chain A: E.109, E.111 Chain B: K.291 Chain C: S.141, K.143, D.144 10 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:E.109, C:K.143, C:D.144, B:K.291 Water bridges: A:E.111, A:Q.117, A:Q.117, C:K.143, C:D.144, B:K.291 B3P.12: 7 residues within 4Å: Chain B: A.363, M.366, T.367, G.382, V.383, R.385, D.386 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.363, B:R.385 B3P.13: 6 residues within 4Å: Chain A: N.469 Chain B: D.489, G.493, V.494, I.495, R.499 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.493, B:R.499, A:N.469 Water bridges: B:D.489, B:D.489, B:S.496, A:K.537, A:K.537 B3P.14: 6 residues within 4Å: Chain A: K.291 Chain B: E.109, E.111 Chain D: S.141, K.143, D.144 7 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:E.109, D:S.141, D:S.141, A:K.291, A:K.291 Water bridges: B:E.111, B:Q.117 B3P.19: 7 residues within 4Å: Chain C: D.489, G.493, V.494, I.495, R.499 Chain D: N.469, K.537 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:N.469, D:K.537, C:G.493, C:R.499 Water bridges: C:G.493, C:S.496 B3P.20: 6 residues within 4Å: Chain C: M.366, T.367, G.382, V.383, R.385, D.386 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.367, C:G.382, C:R.385, C:D.386, C:D.386 B3P.21: 6 residues within 4Å: Chain A: S.141, K.143, D.144 Chain C: E.109, E.111 Chain D: K.291 10 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: A:K.143, A:D.144, D:K.291, C:E.109 Water bridges: A:K.143, A:D.144, A:D.144, C:E.109, C:Q.117, C:Q.117 B3P.26: 7 residues within 4Å: Chain D: A.363, M.366, T.367, G.382, V.383, R.385, D.386 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.363, D:R.385 B3P.27: 6 residues within 4Å: Chain C: N.469 Chain D: D.489, G.493, V.494, I.495, R.499 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:N.469, D:G.493, D:R.499 Water bridges: C:K.537, C:K.537, D:D.489, D:G.493, D:S.496 B3P.28: 6 residues within 4Å: Chain B: S.141, K.143, D.144 Chain C: K.291 Chain D: E.109, E.111 8 PLIP interactions: 3 interactions with chain B, 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:S.141, B:S.141, D:E.109, C:K.291, C:K.291 Water bridges: B:D.144, D:E.109, D:Q.117

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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