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

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z2377835233

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.155, A:N.156 EDO.4: 4 residues within 4Å: Chain A: R.52, M.133, C.140 Chain B: D.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.52

4 x MG: MAGNESIUM ION(Non-covalent)

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

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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