SMTL ID : 5qk0.1 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1270312110

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 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.2 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.2, H2O.2 MG.7: 4 residues within 4Å: Chain B: Q.83, R.85, A.97, E.117 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, H2O.3, H2O.3, H2O.4, H2O.5 MG.8: 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.4, H2O.4

2 x K31: 2-(3,5-dimethyl-1H-pyrazol-4-yl)aniline(Non-covalent)

K31.3: 6 residues within 4Å: Chain A: W.47, E.48 Chain B: W.29, V.30, R.52, L.99 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.29, B:W.29, B:W.29, B:V.30, A:W.47 Hydrogen bonds: B:R.52 pi-Stacking: A:W.47 K31.9: 8 residues within 4Å: Chain A: W.29, V.30, R.52, L.99 Chain B: W.47, E.48, G.136, L.137 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.29, A:W.29, A:V.30, B:E.48 Hydrogen bonds: A:R.52 Water bridges: A:W.29, A:L.99 pi-Stacking: B:W.47

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

EDO.4: 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 A, 1 interactions with chain B Hydrogen bonds: A:R.52 Water bridges: 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 EDO.10: 5 residues within 4Å: Chain A: D.134 Chain B: R.52, M.133, C.140, I.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.52

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

CL.5: 1 residues within 4Å: Chain B: T.146 Ligand excluded by PLIP

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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