5QGN

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with OX-210

• PDB DOI: https://doi.org/10.2210/pdb5QGN/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: 1.95 Å
• R-Value Free: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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: 23.08 kDa 
• Atom Count: 1,691 
• 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
H4D	F [auth A], G [auth A]	3-borono-5-{[(thiophen-2-yl)acetyl]amino}benzoic acid C13 H12 B N O5 S CFVZHOLBBPQSIQ-UHFFFAOYSA-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: 1.95 Å
• R-Value Free:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.179	α = 90
b = 126.179	β = 90
c = 41.665	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