SMTL ID : 3fsj.1

Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-tetramer

Ligands

4 x D7K: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium(Non-covalent)

D7K.1: 30 residues within 4Å: Chain A: H.281, E.375, S.376, T.377, S.378, F.397, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461, F.464 Chain B: N.23, P.24, G.25, S.26, E.47, H.70, N.77, L.110 Ligands: CA.2 26 PLIP interactions: 22 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.377, A:F.397, A:Y.433, A:L.461 Hydrogen bonds: A:T.377, A:T.377, A:S.378, A:S.378, A:S.378, A:S.378, A:G.401, A:L.403, A:G.427, A:G.429, A:S.430, A:Y.433, A:N.455, A:G.459, A:A.460, B:S.26, B:S.26, B:S.26, B:H.70 Water bridges: A:D.428, A:N.455 pi-Stacking: A:H.281 D7K.3: 30 residues within 4Å: Chain A: N.23, P.24, G.25, S.26, E.47, H.70, N.77, L.110 Chain B: H.281, E.375, S.376, T.377, S.378, F.397, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461, F.464 Ligands: CA.4 26 PLIP interactions: 4 interactions with chain A, 22 interactions with chain B Hydrogen bonds: A:S.26, A:S.26, A:S.26, A:H.70, B:T.377, B:T.377, B:S.378, B:S.378, B:S.378, B:S.378, B:G.401, B:L.403, B:G.427, B:G.429, B:S.430, B:Y.433, B:N.455, B:G.459, B:A.460 Hydrophobic interactions: B:T.377, B:F.397, B:Y.433, B:L.461 Water bridges: B:D.428, B:N.455 pi-Stacking: B:H.281 D7K.5: 30 residues within 4Å: Chain C: H.281, E.375, S.376, T.377, S.378, F.397, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461, F.464 Chain D: N.23, P.24, G.25, S.26, E.47, H.70, N.77, L.110 Ligands: CA.6 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:T.377, C:F.397, C:Y.433, C:L.461 Hydrogen bonds: C:T.377, C:T.377, C:S.378, C:S.378, C:S.378, C:S.378, C:G.401, C:L.403, C:G.427, C:G.429, C:S.430, C:N.455, C:G.459, C:A.460, D:S.26, D:S.26, D:S.26, D:H.70 Water bridges: C:D.428, C:N.455 pi-Stacking: C:H.281 D7K.7: 30 residues within 4Å: Chain C: N.23, P.24, G.25, S.26, E.47, H.70, N.77, L.110 Chain D: H.281, E.375, S.376, T.377, S.378, F.397, G.401, G.402, L.403, G.427, D.428, G.429, S.430, Y.433, N.455, T.457, Y.458, G.459, A.460, L.461, F.464 Ligands: CA.8 25 PLIP interactions: 21 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:T.377, D:F.397, D:Y.433, D:L.461 Hydrogen bonds: D:T.377, D:T.377, D:S.378, D:S.378, D:S.378, D:S.378, D:G.401, D:L.403, D:G.427, D:G.429, D:S.430, D:N.455, D:G.459, D:A.460, C:S.26, C:S.26, C:S.26, C:H.70 Water bridges: D:D.428, D:N.455 pi-Stacking: D:H.281

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.428, N.455, T.457 Ligands: D7K.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.428, A:T.457, H2O.3 CA.4: 4 residues within 4Å: Chain B: D.428, N.455, T.457 Ligands: D7K.3 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.428, B:T.457, H2O.22 CA.6: 4 residues within 4Å: Chain C: D.428, N.455, T.457 Ligands: D7K.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.428, C:T.457, H2O.41 CA.8: 4 residues within 4Å: Chain D: D.428, N.455, T.457 Ligands: D7K.7 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.428, D:T.457, H2O.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brandt, G.S. et al., Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry (2009)

Release Date

2009-01-27

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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