SMTL ID : 5qj4.1 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1827602749

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 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: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.113, A:E.167, H2O.1, H2O.1, H2O.2 MG.7: 2 residues within 4Å: Chain B: 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.4, H2O.4, H2O.5, H2O.5 MG.8: 4 residues within 4Å: Chain B: E.113, E.116, E.117, E.167 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.113, B:E.167, H2O.4, H2O.5

2 x K04: (2S,3S)-3-methyl-N-(1,2,3-thiadiazol-5-yl)tetrahydrofuran-2-carboxamide (non-preferred name)(Non-covalent)

K04.3: 6 residues within 4Å: Chain A: W.29, R.52, L.99 Chain B: T.46, W.47, E.48 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.29, A:L.99 pi-Stacking: A:W.29, B:W.47, B:W.47 Hydrogen bonds: B:E.48 Water bridges: B:W.47 K04.9: 4 residues within 4Å: Chain A: W.47, E.48 Chain B: W.29, L.99 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.29, B:L.99 pi-Stacking: B:W.29, A:W.47, A:W.47 Hydrogen bonds: A:E.48

2 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:T.72, B:D.152

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

CL.5: 0 residues within 4Å: (No contacts) 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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