5QGP

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with OX-221

• PDB DOI: https://doi.org/10.2210/pdb5QGP/pdb
• Deposition Group: G_1002045 (changed state) ExploreG_1002045

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


• Deposited: 2018-05-15 Released: 2019-03-27 
• Deposition Author(s): Krojer, T., Talon, R., Fairhead, M., Diaz Saez, L., Bradley, A.R., Aimon, A., Collins, P., Brandao-Neto, J., Douangamath, A., Ruda, G.F., Szommer, T., Srikannathasan, V., Elkins, J., Spencer, J., London, N., Nelson, A., Brennan, P.E., Huber, K., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.224 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

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

Krojer, T., Talon, R., Fairhead, M., Diaz Saez, L., Bradley, A.R., Aimon, A., Collins, P., Brandao-Neto, J., Douangamath, A., Ruda, G.F., Szommer, T., Srikannathasan, V., Elkins, J., Spencer, J., London, N., Nelson, A., Brennan, P.E., Huber, K., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

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: 22.72 kDa 
• Atom Count: 1,647 
• Modelled Residue Count: 186 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal coenzyme A diphosphatase NUDT7	A	196	Homo sapiens	Mutation(s): 0  Gene Names: NUDT7 EC: 3.6.1 (PDB Primary Data), 3.6.1.77 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0C024 (Homo sapiens) Explore P0C024  Go to UniProtKB:  P0C024
PHAROS:  P0C024 GTEx:  ENSG00000140876

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H3Y	F [auth A]	(3aR,4S,6R,7R,8aR)-6-phenyloctahydro-1H-3a,7-epiminocyclohepta[c]pyrrol-4-ol C15 H20 N2 O WNBPFOXFPIFLPO-ZSAUSMIDSA-N
DMS	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	B [auth A], C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.224 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.365	α = 90
b = 126.365	β = 90
c = 41.668	γ = 120

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: 2019-03-27 
Deposition Author(s): Krojer, T., Talon, R., Fairhead, M., Diaz Saez, L., Bradley, A.R., Aimon, A., Collins, P., Brandao-Neto, J., Douangamath, A., Ruda, G.F., Szommer, T., Srikannathasan, V., Elkins, J., Spencer, J., London, N., Nelson, A., Brennan, P.E., Huber, K., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2023-11-15
  Changes: Data collection, Database references