SMTL ID : 6u3j.1

Structure of the 2-oxoadipate dehydrogenase DHTKD1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 21 residues within 4Å: Chain A: H.201, R.202, S.266, H.267, L.268, G.310, D.311, A.312, S.313, Q.317, N.344, L.346, G.347, Y.348, H.413 Chain B: Q.572, L.616, E.618, Q.642, F.646 Ligands: MG.3 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.266, A:L.268, A:D.311, A:A.312, A:S.313, A:L.346, B:Q.572 Water bridges: A:R.202, A:G.310, A:Y.348, A:H.413 Salt bridges: A:H.201, A:R.202, A:H.413 Hydrophobic interactions: B:L.616, B:L.616 pi-Stacking: B:F.646 TPP.4: 21 residues within 4Å: Chain A: Q.572, L.616, E.618, Q.642, F.646 Chain B: H.201, R.202, S.266, H.267, L.268, G.310, D.311, A.312, S.313, Q.317, N.344, L.346, G.347, Y.348, H.413 Ligands: MG.5 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:S.266, B:L.268, B:D.311, B:D.311, B:A.312, B:S.313, B:N.344, B:N.344, A:Q.572 Water bridges: B:R.202, B:G.310, B:D.311, B:Y.348, B:Y.348 Salt bridges: B:H.201, B:R.202, B:H.413 Hydrophobic interactions: A:L.616, A:L.616 pi-Stacking: A:F.646

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.619 Chain B: E.619 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.619, A:E.619, H2O.8, H2O.9, H2O.20 MG.3: 4 residues within 4Å: Chain A: D.311, N.344, L.346 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.311, A:L.346, H2O.4 MG.5: 4 residues within 4Å: Chain B: D.311, N.344, L.346 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.311, B:L.346, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leandro, J. et al., Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex. Acs Chem.Biol. (2020)

Release Date

2020-07-22

Peptides

2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial