SMTL ID : 5qj7.2 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z32327641

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 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.5: 3 residues within 4Å: Chain A: R.52, C.140 Chain B: D.134 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.52 Water bridges: A:R.197, B:D.134, B:D.134, B:D.134 EDO.9: 6 residues within 4Å: Chain A: L.137 Chain B: R.52, D.61, L.99, C.140 Ligands: JMM.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:G.136, B:R.52, B:R.52

4 x MG: MAGNESIUM ION(Non-covalent)

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

2 x JMM: [4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone(Non-covalent)

JMM.4: 9 residues within 4Å: Chain A: T.46, W.47, E.48, G.136, L.137 Chain B: W.29, V.30, D.165 Ligands: EDO.9 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.47, A:L.137, B:W.29, B:V.30 Hydrogen bonds: A:E.48 JMM.8: 9 residues within 4Å: Chain A: W.29, R.52, D.165, G.166 Chain B: T.46, W.47, E.48, G.136, L.137 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.29 Hydrogen bonds: B:E.48

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
C

B
D

ADP-sugar pyrophosphatase

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