5R5R | pdb_00005r5r

PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N14078a

• PDB DOI: https://doi.org/10.2210/pdb5R5R/pdb
• Deposition Group: G_1002128 (changed state) | Explore  G_1002128  

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


• Deposited: 2020-02-28 Released: 2020-07-01 
• Deposition Author(s): Diaz-Saez, L., Talon, R., Krojer, T., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.V.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.234 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Diaz-Saez, L., Talon, R., Krojer, T., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.V.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 33.37 kDa 
• Atom Count: 2,452 
• Modeled Residue Count: 291 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine diphosphate glucose pyrophosphatase NUDT22	A	304	Homo sapiens	Mutation(s): 0  Gene Names: NUDT22, PP11246 EC: 3.6.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRQ3 (Homo sapiens) Explore Q9BRQ3  Go to UniProtKB:  Q9BRQ3
PHAROS:  Q9BRQ3 GTEx:  ENSG00000149761

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S34	B [auth A], C [auth A]	2-cyano-~{N}-(pyridin-4-ylmethyl)ethanamide C9 H9 N3 O ACPRFCGKSGKRCH-UHFFFAOYSA-N
DMS	D [auth A], E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.234 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.54	α = 90
b = 52.3	β = 90
c = 101.85	γ = 90

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: 2020-07-01 
Deposition Author(s): Diaz-Saez, L., Talon, R., Krojer, T., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.V.M.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2026-02-18
  Changes: Refinement description, Structure summary