SMTL ID : 3f6b.1

Crystal structure of benzoylformate decarboxylase in complex with the pyridyl inhibitor PAA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: D.427, N.454, T.456 Ligands: 8PA.2 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.427, B:T.456, H2O.1 MG.3: 4 residues within 4Å: Chain A: D.427, N.454, T.456 Ligands: 8PA.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.427, A:T.456, H2O.18 MG.5: 4 residues within 4Å: Chain D: D.427, N.454, T.456 Ligands: 8PA.6 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.427, D:T.456, H2O.36 MG.7: 4 residues within 4Å: Chain C: D.427, N.454, T.456 Ligands: 8PA.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.427, C:T.456, H2O.54

4 x 8PA: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium(Non-covalent)

8PA.2: 29 residues within 4Å: Chain A: N.22, P.23, G.24, S.25, E.46, H.69, N.76, L.108 Chain B: H.280, E.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460, F.463 Ligands: MG.1 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.432, B:L.460, B:F.463, B:F.463, A:L.108 Hydrogen bonds: B:T.376, B:T.376, B:S.377, B:S.377, B:G.400, B:L.402, B:G.426, B:G.428, B:S.429, B:Y.432, B:N.454, B:T.456, B:G.458, B:A.459, A:S.25, A:S.25 Water bridges: B:D.427, B:N.454, A:H.69 pi-Stacking: B:H.280 8PA.4: 29 residues within 4Å: Chain A: H.280, E.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460, F.463 Chain B: N.22, P.23, G.24, S.25, E.46, H.69, N.76, L.108 Ligands: MG.3 25 PLIP interactions: 21 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.432, A:L.460, A:F.463, A:F.463, B:L.108 Hydrogen bonds: A:T.376, A:T.376, A:S.377, A:S.377, A:G.400, A:L.402, A:G.426, A:G.428, A:S.429, A:Y.432, A:N.454, A:T.456, A:G.458, A:A.459, B:S.25, B:S.25 Water bridges: A:D.427, A:N.454, B:H.69 pi-Stacking: A:H.280 8PA.6: 29 residues within 4Å: Chain C: N.22, P.23, G.24, S.25, E.46, H.69, N.76, L.108 Chain D: H.280, E.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460, F.463 Ligands: MG.5 25 PLIP interactions: 21 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.432, D:L.460, D:F.463, D:F.463, C:L.108 Hydrogen bonds: D:T.376, D:T.376, D:T.376, D:S.377, D:S.377, D:G.400, D:L.402, D:G.426, D:G.428, D:S.429, D:N.454, D:T.456, D:G.458, D:A.459, C:S.25, C:S.25 Water bridges: D:D.427, D:N.454, C:H.69 pi-Stacking: D:H.280 8PA.8: 29 residues within 4Å: Chain C: H.280, E.374, S.375, T.376, S.377, G.400, G.401, L.402, G.426, D.427, G.428, S.429, Y.432, N.454, T.456, Y.457, G.458, A.459, L.460, F.463 Chain D: N.22, P.23, G.24, S.25, E.46, H.69, N.76, L.108 Ligands: MG.7 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.432, C:L.460, C:F.463, C:F.463, D:L.108 Hydrogen bonds: C:T.376, C:T.376, C:T.376, C:S.377, C:S.377, C:G.400, C:L.402, C:G.426, C:G.428, C:S.429, C:N.454, C:T.456, C:G.458, C:A.459, D:S.25, D:S.25 Water bridges: C:D.427, C:N.454, D:H.69 pi-Stacking: C:H.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chakraborty, S. et al., Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry (2009)

Release Date

2008-12-09

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

C
X

D
X

Benzoylformate decarboxylase

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