SMTL ID : 5qjb.1 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1787627869

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: A.97, E.117, E.167 Ligands: MG.2 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.97, A:E.117, H2O.1, H2O.1, H2O.2, H2O.3 MG.2: 4 residues within 4Å: Chain A: E.113, E.117, E.167 Ligands: MG.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.113, A:E.117, A:E.167, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain B: A.97, E.117, E.167 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, H2O.5, H2O.5, H2O.5 MG.9: 4 residues within 4Å: Chain B: E.113, E.116, E.117, E.167 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.113, B:E.167, H2O.5, H2O.5

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x K07: 5-chloro-N-methyl-N-{[(3R)-oxolan-3-yl]methyl}pyrimidin-4-amine(Non-covalent)

K07.4: 6 residues within 4Å: Chain A: W.47, E.48, G.136 Chain B: W.29, R.52, L.99 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.48 pi-Stacking: A:W.47, A:W.47 Halogen bonds: B:R.52 K07.5: 5 residues within 4Å: Chain A: W.29, R.52, L.99 Chain B: W.47, E.48 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B pi-Stacking: A:W.29, B:W.47, B:W.47 Halogen bonds: A:R.52 Hydrogen bonds: B:E.48

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

EDO.6: 5 residues within 4Å: Chain A: R.52, M.133, C.140, I.142 Chain B: D.134 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:D.134 Hydrogen bonds: A:R.52 EDO.7: 3 residues within 4Å: Chain B: Q.70, N.150, D.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.152

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
A

B
B

ADP-sugar pyrophosphatase

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