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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5H025
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
25L (Subject of Investigation/LOI) Query on 25L Download Ideal Coordinates CCD File SDF format, chain C [auth a] SDF format, chain F [auth b] MOL2 format, chain C [auth a] MOL2 format, chain F [auth b]	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		Interactions Focus chain C [auth a] Focus chain F [auth b] Interactions & Density Focus chain C [auth a] Focus chain F [auth b]
MYC (Subject of Investigation/LOI) Query on MYC Download Ideal Coordinates CCD File SDF format, chain D [auth a] SDF format, chain G [auth b] MOL2 format, chain D [auth a] MOL2 format, chain G [auth b]	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		Interactions Focus chain D [auth a] Focus chain G [auth b] Interactions & Density Focus chain D [auth a] Focus chain G [auth b]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth a] MOL2 format, chain E [auth a]	E [auth a]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth a] Interactions & Density Focus chain E [auth a]