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

Crystal structure of the H747A mutant of the SucA domain of Mycobacterium smegmatis KGD showing the active site lid closed

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 19 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, F.323 Chain B: Q.542, L.591, E.593, Q.617, F.621 Ligands: MG.2 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.323 Hydrogen bonds: A:S.245, A:L.247, A:D.286, A:A.287, A:A.288, A:N.319, A:I.321 Water bridges: A:G.285, A:G.285, A:D.286, A:D.286, A:F.323, A:F.323 Salt bridges: A:R.181 pi-Stacking: A:F.323, B:F.621 TPP.5: 19 residues within 4Å: Chain A: Q.542, L.591, E.593, Q.617, F.621 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, F.323 Ligands: MG.6 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.323, A:L.591, A:L.591 Hydrogen bonds: B:S.245, B:L.247, B:A.287, B:A.288, B:N.319 Water bridges: B:R.181, B:R.181, B:G.285, B:D.286, B:D.286, B:F.323 Salt bridges: B:R.181 pi-Stacking: B:F.323, 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: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.286, A:I.321, H2O.4 MG.6: 4 residues within 4Å: Chain B: D.286, N.319, I.321 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.286, B:I.321, H2O.16

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.10, H2O.10 CA.7: 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.20, H2O.20

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 7 residues within 4Å: Chain A: T.679, R.695, D.699, I.701, R.703, Q.783, P.786 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.701 Hydrogen bonds: A:D.699, A:R.703 Water bridges: A:T.679, A:R.703 MPD.8: 6 residues within 4Å: Chain B: T.679, R.695, D.699, R.703, Q.783, P.786 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.699, B:R.703 Water bridges: B:T.679, B:R.703

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
C

B
D

MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME

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