SMTL ID : 5rvy.1

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z437516460

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 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: 16 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:R.203, A:G.311, A:G.311, A:H.414 Salt bridges: A:H.202, A:R.203, A:H.414 pi-Stacking: B:F.647 TPP.5: 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.6 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.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.4 MG.3: 2 residues within 4Å: Chain A: E.620 Chain B: E.620 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:E.620, B:E.620, H2O.4, H2O.15, H2O.44, H2O.55 MG.6: 4 residues within 4Å: Chain B: D.312, N.345, L.347 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.312, B:L.347, H2O.43

1 x NWY: N-[(6-methylpyridin-3-yl)methyl]cyclobutanecarboxamide(Non-covalent)

NWY.4: 11 residues within 4Å: Chain B: A.36, V.39, T.40, C.43, L.84, L.85, Y.100, L.101, I.104, Y.105, A.126 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.36, B:V.39, B:L.84, B:L.85, B:Y.100, B:L.101, B:I.104, B:Y.105 Hydrogen bonds: B:L.84

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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