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

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1497321453

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: K.121, D.123, N.150, D.153, E.155, N.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123, A:D.153, A:E.155, A:N.156 EDO.4: 4 residues within 4Å: Chain A: R.52, M.133, C.140 Chain B: D.134 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.52 Water bridges: A:R.197, B:D.134, B:D.134 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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.97, A:E.117, A:E.167, H2O.2 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.2, H2O.2, H2O.2 MG.5: 3 residues within 4Å: Chain B: A.97, E.117 Ligands: MG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, H2O.4, H2O.4 MG.6: 6 residues within 4Å: Chain B: A.97, G.98, E.113, E.117, E.167 Ligands: MG.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, B:E.167, H2O.3, H2O.4

2 x K0A: (2,5-dimethyl-1,3-thiazol-4-yl)(pyrrolidin-1-yl)methanone(Non-covalent)

K0A.7: 7 residues within 4Å: Chain A: W.29, R.52, L.99 Chain B: W.47, E.48, G.136, L.137 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.29, A:L.99, B:W.47, B:L.137 Hydrogen bonds: A:R.52, A:R.52 K0A.8: 7 residues within 4Å: Chain A: W.47, E.48, G.136, L.137 Chain B: W.29, V.30, R.52 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.29, B:W.29, B:V.30, A:W.47, A:L.137 Hydrogen bonds: B:R.52, B:R.52 pi-Stacking: B:W.29

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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