SMTL ID : 5qk1.1 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z2027049478

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 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.2, H2O.2, H2O.3 MG.2: 4 residues within 4Å: Chain A: E.113, E.117, E.167 Ligands: MG.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.113, A:E.167, H2O.1, H2O.1, H2O.2 MG.7: 3 residues within 4Å: Chain B: A.97, E.117, E.167 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, H2O.4, H2O.4, H2O.5, H2O.5 MG.8: 3 residues within 4Å: Chain B: E.113, E.116, E.167 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.113, B:E.167, H2O.4, H2O.7

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

CL.3: 1 residues within 4Å: Chain B: T.146 Ligand excluded by PLIP

2 x K34: 5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole(Non-covalent)

K34.4: 7 residues within 4Å: Chain A: T.46, W.47, E.48, G.136 Chain B: W.29, V.30, R.52 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.52, A:E.48 pi-Stacking: B:W.29, B:W.29, A:W.47, A:W.47 K34.9: 7 residues within 4Å: Chain A: W.29, V.30, R.52 Chain B: T.46, W.47, E.48, G.136 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.52, B:E.48 Water bridges: A:R.52 pi-Stacking: A:W.29, A:W.29, B:W.47, B:W.47

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

EDO.5: 5 residues within 4Å: Chain A: R.52, M.133, C.140, I.142 Chain B: D.134 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.52 Water bridges: A:R.197, B:D.134 EDO.6: 3 residues within 4Å: Chain B: Q.70, N.150, D.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.152 Water bridges: B:Q.70

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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