7ARA

Deposited: 2020-10-23 Released: 2021-07-28
Deposition Author(s): Deutschmann-Olek, K.M., Skern, T., Bezerra, G.A., Yue, W.W.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

(2021) Virology 562: 128-141

PubMed Abstract:
Picornavirus family members cause disease in humans. Human rhinoviruses (RV), the main causative agents of the common cold, increase the severity of asthma and COPD; hence, effective agents against RVs are required. The 2A proteinase (2A ^pro), found in all enteroviruses, represents an attractive target; inactivating mutations in poliovirus 2A ^pro result in an extension of the VP1 protein preventing infectious virion assembly. Variations in sequence and substrate specificity on eIF4G isoforms between RV 2A ^pro of genetic groups A and B hinder 2A ^pro as drug targets. Here, we demonstrate that although RV-A2 and RV-B4 2A ^pro cleave the substrate GAB1 at different sites, the 2A ^pro from both groups cleave equally efficiently an artificial site containing P1 methionine. We determined the RV-A2 2A ^pro structure complexed with zVAM.fmk, containing P1 methionine. Analysis of this first 2A ^pro-inhibitor complex reveals a conserved hydrophobic P4 pocket among enteroviral 2A ^pro as a potential target for broad-spectrum anti-enteroviral inhibitors.

Organizational Affiliation

Department of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, A-1030, Vienna, Austria.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2A protease	A, B	142	rhinovirus A2	Mutation(s): 0 EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936 Go to UniProtKB: P04936
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S7Q Query on S7Q Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B]	E [auth B]	(phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-[[(2~{R})-1-[[(3~{R})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate C₂₂ H₃₃ N₃ O₅ S XQQSDBOJVLTWFC-LZQZEXGQSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
S7N (Subject of Investigation/LOI) Query on S7N Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(phenylmethyl) ~{N}-[(2~{R})-3-methyl-1-[[(2~{S})-1-[[(3~{S})-1-methylsulfanyl-4-oxidanylidene-pentan-3-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-butan-2-yl]carbamate C₂₂ H₃₃ N₃ O₅ S XQQSDBOJVLTWFC-ZYSHUDEJSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Unit Cell:

Software Package:

Entry History & Funding Information

Deposition Author(s):

Deutschmann-Olek, K.M.

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P28183
Austrian Science Fund	Austria	W1258

Version 1.0: 2021-07-28
Type: Initial release
Version 1.1: 2021-08-04
Changes: Database references
Version 1.2: 2024-01-31
Changes: Data collection, Database references, Refinement description