7JR4

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.180 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.07 kDa 
• Atom Count: 2,704 
• Modelled Residue Count: 299 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	B [auth A], C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Nascimento, A.F.Z., de Oliveira, R.R., Zeri, A.C.M., Trivella, D.B.B.

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Funding Organization	Location	Grant Number
FINEP	Brazil	01.20.0003.00

Revision History  

• 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