SMTL ID : 5rvx.1

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z804566442

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x B0Y: 5-ethyl-~{N}-[(1-methylpyrazol-4-yl)methyl]thiophene-2-carboxamide(Non-covalent)

B0Y.1: 9 residues within 4Å: Chain A: A.353, E.354, R.357, S.358, S.359, L.360 Chain B: N.329, L.330, P.331 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.331, A:E.354, A:L.360 Hydrogen bonds: A:E.354 B0Y.5: 8 residues within 4Å: Chain A: N.329, P.331 Chain B: E.354, R.355, R.357, S.358, S.359, L.360 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.354 Hydrophobic interactions: A:P.331

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 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.3 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.267, A:L.269, A:D.312, A:A.313, A:S.314, A:N.345, A:Y.349 Water bridges: A:H.202, A:R.203, A:G.311, A:G.311, A:N.345, A:H.414, A:H.414 Salt bridges: A:H.202, A:R.203, A:H.414 pi-Stacking: B:F.647 TPP.6: 21 residues within 4Å: Chain A: Q.573, 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.7 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.267, B:L.269, B:D.312, B:D.312, B:A.313, B:S.314, B:N.345, B:Y.349 Water bridges: B:H.202, B:R.203, B:G.311, B:G.311, B:H.414, B:H.414 Salt bridges: B:H.202, B:R.203, B:H.414 pi-Stacking: A:F.647

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.312, N.345, L.347 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.312, A:L.347, H2O.5 MG.4: 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.1, H2O.13, H2O.42, H2O.53 MG.7: 4 residues within 4Å: Chain B: D.312, N.345, L.347 Ligands: TPP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.312, B:L.347, H2O.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezerra, G.A. et al., PanDDA analysis group deposition. To Be Published

Release Date

2020-11-25

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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