5MP0

Human m7GpppN-mRNA Hydrolase (DCP2, NUDT20) Catalytic Domain

• PDB DOI: https://doi.org/10.2210/pdb5MP0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-12-15 Released: 2017-06-28 
• Deposition Author(s): Mathea, S., Salah, E., Velupillai, S., Tallant, C., Pike, A.C.W., Bushell, S.R., Faust, B., Wang, D., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Huber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.262 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Human m7GpppN-mRNA Hydrolase (DCP2, NUDT20) Catalytic Domain

Mathea, S., Huber, K.

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: 19.11 kDa 
• Atom Count: 1,245 
• Modelled Residue Count: 149 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
m7GpppN-mRNA hydrolase	A [auth D]	166	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth D], C [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.262 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.05	α = 90
b = 60.57	β = 90
c = 65.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Mathea, S., Salah, E., Velupillai, S., Tallant, C., Pike, A.C.W., Bushell, S.R., Faust, B., Wang, D., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Huber, K.

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description