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

PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with FS-3764

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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.3, H2O.3, H2O.4 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.3, H2O.4 MG.8: 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.6, H2O.7, H2O.7, H2O.7 MG.9: 4 residues within 4Å: Chain B: R.112, E.113, E.116, E.167 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.116, H2O.6

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

EDO.3: 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.4: 2 residues within 4Å: Chain A: T.105, E.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.105, A:E.107 Water bridges: A:T.105 EDO.7: 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

2 x PWP: 6-fluoroquinazolin-4(3H)-one(Non-covalent)

PWP.5: 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 Hydrogen bonds: B:E.48, B:E.48, A:R.52, A:R.52 pi-Stacking: B:W.47, B:W.47, A:W.29, A:W.29 Hydrophobic interactions: A:W.29 PWP.6: 6 residues within 4Å: Chain A: W.47, E.48, G.136 Chain B: W.29, V.30, R.52 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.48, A:E.48, B:R.52, B:R.52 pi-Stacking: A:W.47, B:W.29, B:W.29 Hydrophobic interactions: B:W.29

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

NUDT5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NUDT5

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