3TNT

Crystal structure of SARS coronavirus main protease complexed with an alpha, beta-unsaturated ethyl ester inhibitor SG85

PDB DOI: https://doi.org/10.2210/pdb3TNT/pdb

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

Deposited: 2011-09-02 Released: 2012-09-05
Deposition Author(s): Zhu, L., Hilgenfeld, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.219
R-Value Work: 0.194
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 34.53 kDa
Atom Count: 2,838
Modelled Residue Count: 306
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G85 Query on G85 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]	N-[(benzyloxy)carbonyl]-O-tert-butyl-L-seryl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide C₃₅ H₄₈ N₄ O₈ JRBUWNJDFCUWEM-CRNKYVSFSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.219
R-Value Work: 0.194
R-Value Observed: 0.195
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.58	α = 90
b = 83.13	β = 104.57
c = 53.32	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):

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

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.