SMTL ID : 6sy1.1

Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 21 residues within 4Å: Chain A: H.202, R.203, S.267, H.268, L.269, G.311, D.312, A.313, S.314, Q.318, N.345, L.347, G.348, Y.349, H.414 Chain B: Q.573, L.617, E.619, Q.643, F.647 Ligands: MG.2 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.267, A:L.269, A:D.312, A:A.313, A:S.314, A:N.345 Water bridges: A:R.203, A:G.311, A:G.311, A:N.345, A:L.347 Salt bridges: A:H.202, A:R.203, A:H.414 Hydrophobic interactions: B:L.617, B:L.617 pi-Stacking: B:F.647 TPP.4: 22 residues within 4Å: Chain A: Q.573, D.574, L.617, E.619, Q.643, F.647 Chain B: H.202, R.203, S.267, H.268, L.269, G.311, D.312, A.313, S.314, Q.318, N.345, L.347, G.348, Y.349, H.414 Ligands: MG.5 13 PLIP interactions: 1 interactions with chain A, 12 interactions with chain B pi-Stacking: A:F.647 Hydrogen bonds: B:S.267, B:L.269, B:D.312, B:A.313, B:S.314, B:N.345 Water bridges: B:R.203, B:G.311, B:G.311 Salt bridges: B:H.202, B:R.203, B:H.414

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.312, N.345, L.347 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.312, A:L.347, H2O.2 MG.3: 2 residues within 4Å: Chain A: E.620 Chain B: E.620 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:E.620, A:E.620, H2O.11, H2O.23, H2O.26, H2O.31 MG.5: 4 residues within 4Å: Chain B: D.312, N.345, L.347 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.312, B:L.347, H2O.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezerra, G.A. et al., Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism. Iucrj (2020)

Release Date

2020-06-24

Peptides

Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial

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