SMTL ID : 2xt6.1

Crystal structure of Mycobacterium smegmatis alpha-ketoglutarate decarboxylase homodimer (orthorhombic form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 20 residues within 4Å: Chain A: R.426, S.490, H.491, L.492, G.530, D.531, A.532, A.533, Q.537, N.564, I.566, G.567, F.568, H.633 Chain B: Q.787, L.836, E.838, Q.862, F.866 Ligands: MG.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.568 Hydrogen bonds: A:S.490, A:L.492, A:D.531, A:A.532, A:A.533, A:N.564 Water bridges: A:G.530, A:F.568, A:H.633 Salt bridges: A:R.426 pi-Stacking: B:F.866 TPP.4: 19 residues within 4Å: Chain A: Q.787, L.836, E.838, Q.862, F.866 Chain B: R.426, S.490, H.491, L.492, G.530, D.531, A.532, A.533, Q.537, N.564, I.566, G.567, H.633 Ligands: MG.5 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:L.836, A:L.836 pi-Stacking: A:F.866 Hydrogen bonds: B:S.490, B:L.492, B:D.531, B:A.532, B:A.533, B:N.564, B:I.566 Water bridges: B:R.426, B:G.530, B:H.633 Salt bridges: B:R.426, B:H.633

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.531, N.564, I.566 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.531, A:I.566, H2O.1 MG.5: 4 residues within 4Å: Chain B: D.531, N.564, I.566 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.531, B:I.566, H2O.5

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.890, H.941, D.944, I.946 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.890, A:H.941, A:D.944, A:I.946, H2O.2 CA.6: 4 residues within 4Å: Chain B: D.890, H.941, D.944, I.946 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.890, B:H.941, B:D.944, B:I.946, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism. Chem.Biol. (2011)

Release Date

2011-06-15

Peptides

2-OXOGLUTARATE DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-OXOGLUTARATE DECARBOXYLASE