SMTL ID : 5qj5.1 (1 other biounit)

PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with Z44592329

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

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

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x K0G: N-phenyl-N'-pyridin-3-ylurea(Non-covalent)

K0G.4: 15 residues within 4Å: Chain A: V.30, V.50, K.51, R.52, G.62, V.63, A.97, G.98, L.99, M.133, C.140, I.142, R.197 Chain B: D.134, L.137 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.137, A:V.30, A:R.52, A:A.97, A:L.99, A:I.142 Hydrogen bonds: B:D.134, B:D.134, A:R.52 K0G.8: 15 residues within 4Å: Chain A: D.134, L.137 Chain B: V.30, V.50, K.51, R.52, G.62, V.63, A.97, G.98, L.99, M.133, C.140, I.142, R.197 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.137, B:V.30, B:A.97, B:L.99, B:I.142 Hydrogen bonds: A:D.134, A:D.134, B:R.52

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

EDO.5: 3 residues within 4Å: Chain B: Q.70, N.150, D.152 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.72, B:D.152 Water bridges: B:Q.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubianok, Y. et al., PanDDA analysis group deposition. To Be Published

Release Date

2018-12-19

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-sugar pyrophosphatase

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