SMTL ID : 5qtl.2 (1 other biounit)

PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with GB-0804

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: K.121, D.123, N.150, D.153, E.155, N.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.123, A:N.156 EDO.4: 4 residues within 4Å: Chain A: R.52, M.133, C.140 Chain B: D.134 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.52 Water bridges: A:R.197, B:D.134, B:D.134 EDO.6: 5 residues within 4Å: Chain A: D.134 Chain B: R.52, M.133, C.140, I.142 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.52 Water bridges: B:R.197, A:D.134, A:D.134, A:D.134

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: A.97, E.113, E.117, E.167 Ligands: MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.113, A:E.117, H2O.1, H2O.2, H2O.3 MG.3: 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.2, H2O.2, H2O.2, H2O.3 MG.8: 5 residues within 4Å: Chain B: A.97, E.113, E.117, E.167 Ligands: MG.9 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.5 MG.9: 6 residues within 4Å: Chain B: A.97, G.98, E.113, E.117, E.167 Ligands: MG.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.113, B:E.117, B:E.167, H2O.4, H2O.5

2 x PW7: 4-(trifluoromethyl)pyrimidin-2-amine(Non-covalent)

PW7.5: 5 residues within 4Å: Chain A: W.29, L.99 Chain B: W.47, E.48, G.136 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.48, B:E.48 pi-Stacking: B:W.47, B:W.47, A:W.29 pi-Cation interactions: B:W.47 PW7.7: 7 residues within 4Å: Chain A: W.47, E.48, G.136 Chain B: W.29, V.30, R.52, L.99 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.48, A:E.48, B:R.52 pi-Stacking: A:W.47, A:W.47, B:W.29 pi-Cation interactions: A:W.47 Hydrophobic interactions: B:W.29 Water bridges: 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

NUDT5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

NUDT5

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