Macromolecule Content

Total Structure Weight: 67.84 kDa
Atom Count: 4940
Modelled Residue Count: 612
Deposited Residue Count: 612
Unique protein chains: 1

6XKF

The crystal structure of 3CL MainPro of SARS-CoV-2 with oxidized Cys145 (Sulfenic acid cysteine).

PDB DOI: 10.2210/pdb6XKF/pdb

Classification: HYDROLASE
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-26 Released: 2020-07-08
Deposition Author(s): Tan, K., Maltseva, N.I., Welk, L.F., Jedrzejczak, R.P., Coates, L., Kovalevskyi, A.Y., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.239
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of 3CL MainPro of SARS-CoV-2 with oxidized Cys145 (Sulfenic acid cysteine).

Tan, K., Maltseva, N.I., Welk, L.F., Jedrzejczak, R.P., Coates, L., Kovalevskyi, A.Y., Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX Query on CSX	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.239
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.878	α = 90
b = 53.791	β = 100.97
c = 115.261	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-06-26
Released Date: 2020-07-08

Deposition Author(s):

Jedrzejczak, R.P.

Kovalevskyi, A.Y.

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.