SMTL ID : 5qk2.1 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z54628578

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

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

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

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

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

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

1 x JH4: N-methylpyrimidin-2-amine(Non-covalent)

JH4.8: 6 residues within 4Å: Chain A: W.29, V.30, R.52 Chain B: W.47, E.48, G.136 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.29 Water bridges: A:R.52 pi-Stacking: A:W.29, B:W.47, B:W.47 Hydrogen bonds: B:E.48, B:E.48

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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