3TNS

Crystal structure of SARS coronavirus main protease complexed with an alpha, beta-unsaturated ethyl ester inhibitor SG83

PDB DOI: https://doi.org/10.2210/pdb3TNS/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Severe acute respiratory syndrome-related coronavirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-09-01 Released: 2012-09-05
Deposition Author(s): Zhu, L., Hilgenfeld, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.245
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structures of SARS-Cov main protease complexed with a series of peptidic unsaturated esters

Zhu, L., Hilgenfeld, R.

To be published.

Macromolecule Content

Total Structure Weight: 34.56 kDa
Atom Count: 2,624
Modelled Residue Count: 306
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS coronavirus main protease	A	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0 EC: 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7 Go to UniProtKB: P0C6X7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C6X7
Sequence AnnotationsExpand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G83 Query on G83 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ETHYL (5S,8S,11R)-8-BENZYL-5-(2-TERT-BUTOXY-2-OXOETHYL)-3,6,9-TRIOXO-11-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}-1-PHENYL-2-OXA-4,7,10-TRIAZATETRADECAN-14-OATE C₃₆ H₄₈ N₄ O₉ DAQSBCFYXOITIO-CRNKYVSFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.245
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.31	α = 90
b = 82.86	β = 104.69
c = 53.33	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Zhu, L.

Hilgenfeld, R.

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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