SMTL ID : 2yid.1 (1 other biounit)

Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with the enamine-ThDP intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x TD7: (4E)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-2(3H)-ylidene}-4-hydroxybutanoic acid(Non-covalent)

TD7.1: 24 residues within 4Å: Chain A: F.147, H.180, R.181, Y.219, H.220, S.245, H.246, L.247, G.285, D.286, A.287, A.288, Q.292, N.319, I.321, G.322, H.388 Chain B: Q.542, L.591, E.593, Q.617, F.621, H.661 Ligands: MG.2 20 PLIP interactions: 3 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:Q.542, A:S.245, A:L.247, A:A.287, A:A.288, A:N.319 Salt bridges: B:H.661, A:H.180, A:R.181, A:H.220, A:H.388 pi-Stacking: B:F.621 Hydrophobic interactions: A:F.147 Water bridges: A:H.180, A:R.181, A:R.181, A:S.245, A:G.285, A:D.286, A:D.286 TD7.4: 24 residues within 4Å: Chain A: Q.542, L.591, E.593, Q.617, F.621, H.661 Chain B: F.147, H.180, R.181, Y.219, H.220, S.245, H.246, L.247, G.285, D.286, A.287, A.288, Q.292, N.319, I.321, G.322, H.388 Ligands: MG.5 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.147 Hydrogen bonds: B:S.245, B:L.247, B:D.286, B:A.287, B:A.288, B:N.319 Water bridges: B:R.181, B:R.181, B:S.245, B:G.285, B:G.285, B:D.286, B:D.286 Salt bridges: B:H.180, B:R.181, B:H.220, B:H.388, A:H.661 pi-Stacking: A:F.621

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.286, N.319, I.321 Ligands: TD7.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.286, A:I.321, H2O.2 MG.5: 4 residues within 4Å: Chain B: D.286, N.319, I.321 Ligands: TD7.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.286, B:I.321, H2O.10

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.645, H.696, D.699, I.701 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.696, A:D.699, A:I.701, H2O.6, H2O.6 CA.6: 4 residues within 4Å: Chain B: D.645, H.696, D.699, I.701 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.696, B:D.699, B:I.701, H2O.13, H2O.13

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

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