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

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z57292369

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 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.3, H2O.3 MG.2: 5 residues within 4Å: Chain A: A.97, 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.117, A:E.167, H2O.1, H2O.1, H2O.3 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.4, H2O.5, H2O.6 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.5, H2O.5

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x K41: 2-methyl-N-(2-methyl-2H-tetrazol-5-yl)propanamide(Non-covalent)

K41.4: 6 residues within 4Å: Chain A: W.47, E.48, G.136 Chain B: W.29, V.30, L.99 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.29, B:W.29, B:L.99, A:W.47 Water bridges: B:W.29, B:R.52, B:R.52 pi-Stacking: B:W.29, A:W.47, A:W.47 Hydrogen bonds: A:E.48 K41.8: 6 residues within 4Å: Chain A: W.29, V.30, R.52 Chain B: W.47, E.48, G.136 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.47, A:W.29, A:W.29 Hydrogen bonds: B:E.48, A:R.52 pi-Stacking: B:W.47, B:W.47, A:W.29 Water bridges: A:W.29

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

EDO.5: 4 residues within 4Å: Chain B: Q.70, T.72, N.150, D.152 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.72, B:D.152 Water bridges: B:Q.70 EDO.9: 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

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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