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

PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with 8J-537S

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: 4 residues within 4Å: Chain A: A.97, E.117, E.167 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.113, A:E.117, H2O.1, H2O.1, H2O.3 MG.10: 3 residues within 4Å: Chain B: A.97, E.117 Ligands: MG.11 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.11: 5 residues within 4Å: Chain B: A.97, E.113, E.117, E.167 Ligands: MG.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.113, B:E.117, B:E.167, H2O.5, H2O.6

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

CL.3: 1 residues within 4Å: Chain B: V.68 Ligand excluded by PLIP

2 x PWS: 3-methyl-2-(methylsulfanyl)-6-(trifluoromethyl)pyrimidin-4(3H)-one(Non-covalent)

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

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

EDO.5: 5 residues within 4Å: Chain A: R.52, M.133, C.140, I.142 Chain B: D.134 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.52 Water bridges: A:R.197, B:D.134 EDO.6: 5 residues within 4Å: Chain A: Q.70, R.71, T.72, N.150, D.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.152 Water bridges: A:Q.70 EDO.7: 3 residues within 4Å: Chain A: T.46 Chain B: W.29 Ligands: PWS.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.46, A:T.46 EDO.9: 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 EDO.12: 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. To Be Published

Release Date

2019-12-25

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-sugar pyrophosphatase

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