7ELW

Crystal structure of RNase L in complex with Myricetin

• PDB DOI: https://doi.org/10.2210/pdb7ELW/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-04-12 Released: 2021-11-24 
• Deposition Author(s): Tang, J., Huang, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 0.280 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

Starting Model: experimental

Literature

Identification of Small Molecule Inhibitors of RNase L by Fragment-Based Drug Discovery

Tang, J., Dong, B., Liu, M., Liu, S., Niu, X., Gaughan, C., Asthana, A., Zhou, H., Xu, Z., Zhang, G., Silverman, R.H., Huang, H.

(2022) J Med Chem 65: 1445-1457

• DOI: https://doi.org/10.1021/acs.jmedchem.1c01156

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 165.72 kDa 
• Atom Count: 10,909 
• Modelled Residue Count: 1,351 
• Deposited Residue Count: 1,434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease L	A [auth a], B [auth b]	717	Sus scrofa	Mutation(s): 0  Gene Names: RNASEL
UniProt
Find proteins for A5H025 (Sus scrofa) Explore A5H025  Go to UniProtKB:  A5H025

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
25L (Subject of Investigation/LOI)	C [auth a], F [auth b]	[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate C30 H40 N15 O25 P5 RTAGLZBJCCVJET-UQTMIEBXSA-N
MYC (Subject of Investigation/LOI)	D [auth a], G [auth b]	3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE C15 H10 O8 IKMDFBPHZNJCSN-UHFFFAOYSA-N
PO4	E [auth a]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.55 Å
• R-Value Free: 0.280 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.608	α = 90
b = 111.925	β = 90
c = 264.929	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Tang, J., Huang, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21778808

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2022-06-08
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description