SMTL ID : 5rw0.1

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z2444997446

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

5 x WGD: 1-{(2S,4S)-4-fluoro-1-[(2-methyl-1,3-thiazol-4-yl)methyl]pyrrolidin-2-yl}methanamine(Non-covalent)

WGD.1: 9 residues within 4Å: Chain A: Q.285, D.291, Y.292, S.293, P.294, N.600, F.609, L.610, E.611 No protein-ligand interaction detected (PLIP) WGD.2: 6 residues within 4Å: Chain A: R.287, Q.288, S.293, P.294, D.295, R.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.293 Water bridges: A:R.303, A:R.303 pi-Cation interactions: A:R.303 WGD.3: 7 residues within 4Å: Chain A: A.353, E.354, R.357, S.358, S.359, L.360 Chain B: N.329 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:N.329, A:E.354 Water bridges: B:N.329, A:S.358, A:L.360 WGD.6: 9 residues within 4Å: Chain B: Q.285, D.291, Y.292, S.293, P.294, N.600, F.609, L.610, E.611 No protein-ligand interaction detected (PLIP) WGD.7: 6 residues within 4Å: Chain A: N.329 Chain B: E.354, R.357, S.358, S.359, L.360 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:S.358, B:L.360, A:K.400

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 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.5 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:L.347 Water bridges: A:H.202, A:R.203, A:G.311, A:G.311, A:Y.349, A:H.414 Salt bridges: A:H.202, A:R.203, A:H.414 pi-Stacking: B:F.647 TPP.8: 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.9 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.5: 4 residues within 4Å: Chain A: D.312, N.345, L.347 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.312, A:L.347, H2O.6 MG.9: 4 residues within 4Å: Chain B: D.312, N.345, L.347 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.312, B:L.347, H2O.41 MG.10: 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.2, H2O.18, H2O.43, H2O.53

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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