SMTL ID : 5qj9.1 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z768399682

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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.2, H2O.2, H2O.3 MG.2: 5 residues within 4Å: Chain A: E.113, E.116, E.117, E.167 Ligands: MG.1 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.113, A:E.117, A:E.167, H2O.1, H2O.2, H2O.2 MG.7: 4 residues within 4Å: Chain B: A.97, G.98, E.117 Ligands: MG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, H2O.4, H2O.4, H2O.6 MG.8: 6 residues within 4Å: Chain B: A.97, E.113, E.116, E.117, E.167 Ligands: MG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.113, B:E.117, H2O.4, H2O.4

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

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

2 x K0D: [(2R,5S)-2,5-dimethylmorpholin-4-yl](1,2,5-thiadiazol-3-yl)methanone(Non-covalent)

K0D.4: 5 residues within 4Å: Chain A: W.47, E.48 Chain B: W.29, R.52, L.99 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.47, B:W.29, B:L.99 Hydrogen bonds: A:E.48, B:R.52 pi-Stacking: A:W.47 K0D.9: 7 residues within 4Å: Chain A: W.29, V.30, R.52, L.99 Chain B: W.47, E.48, G.136 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.99, B:W.47 Hydrogen bonds: A:R.52, B:E.48 Water bridges: A:R.52 pi-Stacking: B:W.47

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

EDO.5: 6 residues within 4Å: Chain A: N.177, D.178, L.179, L.180, Q.181, K.206 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.178, A:D.178, A:L.180, A:Q.181 Water bridges: A:N.177, A:L.179, A:L.179, A:K.206 EDO.6: 4 residues within 4Å: Chain B: Q.70, R.71, N.150, D.152 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.72, B:G.151, B:D.152 Water bridges: B:Q.70

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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