7JR4 | pdb_00007jr4

SARS-CoV-2 3CL protease with alternative conformation of the active site promoted by methylene-bridged cysteine and lysine residues

PDB DOI: https://doi.org/10.2210/pdb7JR4/pdb

Classification: HYDROLASE
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-11 Released: 2020-08-26
Deposition Author(s): Nascimento, A.F.Z., de Oliveira, R.R., Zeri, A.C.M., Trivella, D.B.B.
Funding Organization(s): FINEP

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.180 (Depositor), 0.180 (DCC)
R-Value Work:
0.153 (Depositor), 0.150 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

SARS-CoV-2 3CL protease with alternative conformation of the active site promoted by methylene-bridged cysteine and lysine residues

Nascimento, A.F.Z., de Oliveira, R.R., Zeri, A.C.M., Trivella, D.B.B.

To be published.

Macromolecule Content

Total Structure Weight: 34.07 kDa
Atom Count: 2,704
Modeled Residue Count: 299
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
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69
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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ Query on MLZ	A	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.180 (Depositor), 0.180 (DCC)
R-Value Work: 0.153 (Depositor), 0.150 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.153	α = 90
b = 82.353	β = 114.62
c = 51.59	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Nascimento, A.F.Z.

de Oliveira, R.R.

Trivella, D.B.B.

Funding Organization	Location	Grant Number
FINEP	Brazil	01.20.0003.00

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2023-07-19
Changes: Data collection, Database references
Version 1.2: 2023-10-25
Changes: Data collection, 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.