SMTL ID : 6r2c.1 (1 other biounit)

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate phosphonoethyl ester (PESP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.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 Ligands: MG.2, JQ5.4 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.245, A:L.247, A:D.286, A:A.287, A:A.288, A:N.319, A:H.388 Water bridges: A:R.181, A:G.285, A:D.286, A:D.286, A:F.323, A:F.323 Salt bridges: A:R.181 pi-Stacking: B:F.621 TPP.5: 20 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, H.388 Ligands: MG.6, JQ5.8 13 PLIP interactions: 10 interactions with chain B, 3 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:G.285, B:F.323, B:F.323 Salt bridges: B:R.181 Hydrophobic interactions: A:L.591, 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: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.286, A:I.321, H2O.1 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.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.1, H2O.6 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.11, H2O.15

2 x JQ5: 4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanylidene-butanoic acid(Non-covalent)

JQ5.4: 13 residues within 4Å: Chain A: R.146, H.180, H.220, S.245, F.323, H.388, N.389 Chain B: T.548, Q.617, F.618, F.621, H.661 Ligands: TPP.1 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.323, B:T.548, B:F.618 Hydrogen bonds: A:R.146, B:H.661 Water bridges: A:H.180, A:H.180 Salt bridges: A:H.180, A:H.220, B:H.661 JQ5.8: 13 residues within 4Å: Chain A: T.548, Q.617, F.618, F.621, H.661 Chain B: R.146, H.180, H.220, S.245, F.323, H.388, N.389 Ligands: TPP.5 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.323, A:T.548, A:F.618 Hydrogen bonds: B:R.146, A:H.661 Water bridges: B:H.180, B:H.180 Salt bridges: B:H.180, B:H.220, A:H.661

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts. J.Struct.Biol. (2019)

Release Date

2019-09-11

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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