5QP9

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z100435060

• PDB DOI: https://doi.org/10.2210/pdb5QP9/pdb
• Deposition Group: G_1002061 (changed state) ExploreG_1002061

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


• Deposited: 2019-02-22 Released: 2019-05-08 
• Deposition Author(s): Nelson, E.R., Velupillai, S., Talon, R., Collins, P.M., Krojer, T., Wang, D., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Huber, K., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.253 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

PanDDA analysis group deposition

Nelson, E.R., Velupillai, S., Talon, R., Collins, P.M., Krojer, T., Wang, D., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Huber, K., 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: 19.64 kDa 
• Atom Count: 1,328 
• Modelled Residue Count: 149 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DCP2 (NUDT20)	A	167	Homo sapiens	Mutation(s): 0  Gene Names: DCP2, NUDT20 EC: 3.6.1.62
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU60 (Homo sapiens) Explore Q8IU60  Go to UniProtKB:  Q8IU60
PHAROS:  Q8IU60 GTEx:  ENSG00000172795

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LJD	G [auth A]	N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazole-4-carboxamide C12 H12 Cl N3 O LBSYJSKGYMMGBC-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	E [auth A], F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.253 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.406	α = 90
b = 60.406	β = 90
c = 65.58	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: 2019-05-08 
Deposition Author(s): Nelson, E.R., Velupillai, S., Talon, R., Collins, P.M., Krojer, T., Wang, D., Brandao-Neto, J., Douangamath, A., Burgess-Brown, N., Arrowsmith, C.H., Bountra, C., Huber, K., von Delft, F.

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Data collection
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references