5QJ8

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z2856434829

• PDB DOI: https://doi.org/10.2210/pdb5QJ8/pdb
• Deposition Group: G_1002057 (changed state) ExploreG_1002057

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-31 Released: 2018-12-19 
• Deposition Author(s): Dubianok, Y., Collins, P., Krojer, T., Wright, N., Strain-Damerell, C., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.278 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 

Literature

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)

Dubianok, Y., Collins, P., Krojer, T., Wright, N., Strain-Damerell, C., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.14 kDa 
• Atom Count: 5,997 
• Modelled Residue Count: 770 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-sugar pyrophosphatase	A, B, C, D	209	Homo sapiens	Mutation(s): 0  Gene Names: NUDT5, NUDIX5, HSPC115 EC: 3.6.1.13 (PDB Primary Data), 3.6.1.58 (PDB Primary Data), 2.7.7.96 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKK9 (Homo sapiens) Explore Q9UKK9  Go to UniProtKB:  Q9UKK9
PHAROS:  Q9UKK9 GTEx:  ENSG00000165609

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ELQ	K [auth B]	[3,4-bis(fluoranyl)phenyl]-(4-methylpiperazin-1-yl)methanone C12 H14 F2 N2 O ZCPNSVBDWJVJSY-UHFFFAOYSA-N
EDO	H [auth B], L [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], O [auth D], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.278 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.53	α = 79.56
b = 59.99	β = 81.09
c = 79.65	γ = 75.49

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Dubianok, Y., Collins, P., Krojer, T., Wright, N., Strain-Damerell, C., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F.

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-30
  Changes: Structure summary