SMTL ID : 5rvw.1

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z1587220559

Coordinates

PDB Format Compare

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 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:H.202, 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.4: 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.5 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.3 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.44 MG.6: 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.1, H2O.6, H2O.12, H2O.55

1 x T1J: 2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol(Non-covalent)

T1J.3: 7 residues within 4Å: Chain B: D.508, L.509, F.512, A.563, M.602, D.603, Q.606 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.508, B:L.509, B:L.509, B:F.512, B:F.512, B:A.563, B:M.602, B:D.603, B:Q.606 Hydrogen bonds: B:D.603

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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