SMTL ID : 4q9d.1

X-ray structure of a putative thiamin diphosphate-dependent enzyme isolated from Mycobacterium smegmatis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: G.433, D.434, L.459, N.461, E.463 Ligands: FMT.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.434 MG.4: 4 residues within 4Å: Chain B: D.434, N.461, E.463 Ligands: FMT.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.434, B:E.463, H2O.22, H2O.29 MG.7: 6 residues within 4Å: Chain C: G.433, D.434, L.459, N.461, E.463 Ligands: FMT.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.434 MG.10: 4 residues within 4Å: Chain D: D.434, N.461, E.463 Ligands: FMT.12 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.434, D:E.463, H2O.57, H2O.64

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 4 residues within 4Å: Chain A: Y.146, S.178, V.179, T.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.179, A:V.179 FMT.3: 7 residues within 4Å: Chain A: G.433, D.434, G.435, S.436, E.463, Y.464 Ligands: MG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.434, A:G.435, A:S.436, A:S.436 FMT.5: 4 residues within 4Å: Chain B: Y.146, M.150, S.178, V.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.179, B:V.179 FMT.6: 7 residues within 4Å: Chain B: G.433, D.434, G.435, S.436, E.463, Y.464 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.434, B:G.435, B:S.436, B:E.463, B:A.465 Water bridges: B:T.379, B:T.379, B:D.434 FMT.8: 4 residues within 4Å: Chain C: Y.146, S.178, V.179, T.181 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.146, C:V.179, C:V.179 FMT.9: 7 residues within 4Å: Chain C: G.433, D.434, G.435, S.436, E.463, Y.464 Ligands: MG.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.435, C:S.436, C:S.436 FMT.11: 4 residues within 4Å: Chain D: Y.146, M.150, S.178, V.179 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.146, D:V.179, D:V.179 FMT.12: 7 residues within 4Å: Chain D: G.433, D.434, G.435, S.436, E.463, Y.464 Ligands: MG.10 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.435, D:S.436, D:E.463, D:A.465 Water bridges: D:T.379, D:T.379, D:D.434

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrews, F.H. et al., The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes. Biochim.Biophys.Acta (2015)

Release Date

2015-04-29

Peptides

Benzoylformate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Benzoylformate decarboxylase