SMTL ID : 5qjk.2 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z373221060

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: D.123, N.150, D.153, E.155, N.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.155, A:E.155, A:N.156 Water bridges: A:N.150 EDO.5: 5 residues within 4Å: Chain A: R.52, M.133, C.140, I.142 Chain B: D.134 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:D.134, B:D.134, A:R.197 Hydrogen bonds: A:R.52 EDO.9: 5 residues within 4Å: Chain A: D.134 Chain B: R.52, M.133, C.140, I.142 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.52 Water bridges: B:R.197, A:D.134, A:D.134

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: A.97, G.98, E.113, E.117, E.167 Ligands: MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.97, A:E.117, H2O.3 MG.3: 4 residues within 4Å: Chain A: A.97, E.117, E.167 Ligands: MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.97, A:E.117, H2O.1, H2O.1, H2O.3 MG.6: 3 residues within 4Å: Chain B: A.97, E.117 Ligands: MG.7 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, H2O.4, H2O.5, H2O.5, H2O.5 MG.7: 6 residues within 4Å: Chain B: A.97, G.98, E.113, E.117, E.167 Ligands: MG.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.97, B:E.113, B:E.117, H2O.5

2 x K1D: 6-(azetidin-1-yl)-9H-purine(Non-covalent)

K1D.4: 6 residues within 4Å: Chain A: W.47, E.48, G.136 Chain B: W.29, R.52, L.99 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.48, A:E.48, B:R.52, B:R.52 pi-Stacking: A:W.47, A:W.47, B:W.29 Hydrophobic interactions: B:W.29, B:L.99 K1D.8: 6 residues within 4Å: Chain A: W.29, R.52, L.99 Chain B: W.47, E.48, G.136 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.29, A:L.99 Hydrogen bonds: A:R.52, A:R.52, B:E.48, B:E.48 pi-Stacking: A:W.29, B:W.47, B:W.47, B:W.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubianok, Y. et al., PanDDA analysis group deposition of models with modelled events (e.g. bound ligands). To Be Published

Release Date

2018-12-19

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

ADP-sugar pyrophosphatase

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