SMTL ID : 3zhv.2 (1 other biounit)

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x TDW: 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-[(1S)-1-oxidanylethyl]-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate(Non-covalent)

TDW.1: 20 residues within 4Å: Chain A: R.181, 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 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.245, A:L.247, A:A.287, A:A.288, A:N.319 Water bridges: A:R.181, A:G.285, A:G.285, A:D.286, A:D.286 Salt bridges: A:R.181, A:H.388 pi-Stacking: B:F.621 TDW.4: 20 residues within 4Å: Chain A: Q.542, L.591, E.593, Q.617, F.621, H.661 Chain B: R.181, 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 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A 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:G.285 Salt bridges: B:R.181 Hydrophobic interactions: A:L.591 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: TDW.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.286, A:I.321, H2O.3 MG.5: 4 residues within 4Å: Chain B: D.286, N.319, I.321 Ligands: TDW.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.286, B:I.321, H2O.14

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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.645, A:D.645, A:H.696, A:I.701, H2O.8 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:D.645, B:D.645, B:H.696, H2O.18, H2O.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., A Dual Conformation of the Post-Decarboxylation Intermediate is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd). Biochem.J. (2014)

Release Date

2013-11-13

Peptides

MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME

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