8DMT

Crystal structure of macrodomain CG2909 from Drosophila melanogaster in complex with ADP-ribose

• PDB DOI: https://doi.org/10.2210/pdb8DMT/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-08 Released: 2023-08-02 
• Deposition Author(s): Zhang, Z., Das, C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Structure of ADP-ribose-bound Drosophila macrodomain CG2909

Zhang, Z., Das, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 224.15 kDa 
• Atom Count: 15,829 
• Modelled Residue Count: 1,950 
• Deposited Residue Count: 1,968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RE54994p	A, B, C, D	492	Drosophila melanogaster	Mutation(s): 0  Gene Names: Dmel\CG2909, CG2909, Dmel_CG2909
UniProt
Find proteins for Q9W2W5 (Drosophila melanogaster) Explore Q9W2W5  Go to UniProtKB:  Q9W2W5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.949	α = 90
b = 90.006	β = 95.89
c = 212.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Zhang, Z., Das, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01GM126296
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI148103

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release