SMTL ID : 5qj6.2 (1 other biounit)

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1614545742

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123, A:D.153, A:E.155, A:N.156 EDO.4: 4 residues within 4Å: Chain A: R.52, M.133, C.140 Chain B: D.134 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:D.134, B:D.134 Hydrogen bonds: A:R.52 EDO.8: 5 residues within 4Å: Chain A: D.134 Chain B: R.52, M.133, C.140, I.142 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:D.134, A:D.134, B:R.197 Hydrogen bonds: B:R.52

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

1 x GQJ: methyl (2~{S},4~{R})-1-(furan-2-ylcarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylate(Non-covalent)

GQJ.7: 12 residues within 4Å: Chain A: K.206, H.207 Chain B: I.66, V.68, Q.70, A.125, E.126, T.146, V.147, T.148, K.176, Y.201 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.68, B:T.148 Water bridges: B:K.176 Hydrogen bonds: A:K.206, A:K.206 pi-Cation interactions: A:H.207

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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