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

Ground-state model of NUDT5 and corresponding apo datasets for PanDDA analysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 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.1, H2O.2, H2O.2 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.1, H2O.2 MG.5: 4 residues within 4Å: Chain B: A.97, E.117, E.167 Ligands: MG.6 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.97, B:E.117, H2O.3, H2O.4, H2O.4, H2O.4 MG.6: 6 residues within 4Å: Chain B: A.97, E.113, E.116, E.117, E.167 Ligands: MG.5 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.113, B:E.167, H2O.3, H2O.4, H2O.5

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

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

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

EDO.4: 3 residues within 4Å: Chain B: Q.70, N.150, D.152 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: 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 of ground-state model. To Be Published

Release Date

2020-04-29

Peptides

ADP-sugar pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-sugar pyrophosphatase

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