7LDX

SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.

Noske, G.D.Nakamura, A.M.Gawriljuk, V.O.Fernandes, R.S.Lima, G.M.A.Rosa, H.V.D.Pereira, H.D.Zeri, A.C.M.Nascimento, A.F.Z.Freire, M.C.L.C.Fearon, D.Douangamath, A.von Delft, F.Oliva, G.Godoy, A.S.

(2021) J Mol Biol 433: 167118-167118

  • DOI: https://doi.org/10.1016/j.jmb.2021.167118
  • Primary Citation of Related Structures:  
    7KFI, 7KPH, 7KVL, 7KVR, 7LDX, 7LFE, 7LFP, 7MBG, 7N5Z, 7N6N

  • PubMed Abstract: 

    SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral M pro is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. The lack of structural information for intermediary forms of M pro is a setback for the understanding its self-maturation process. Herein, we used X-ray crystallography combined with biochemical data to characterize multiple forms of SARS-CoV-2 M pro . For the immature form, we show that extra N-terminal residues caused conformational changes in the positioning of domain-three over the active site, hampering the dimerization and diminishing its activity. We propose that this form preludes the cis and trans-cleavage of N-terminal residues. Using fragment screening, we probe new cavities in this form which can be used to guide therapeutic development. Furthermore, we characterized a serine site-directed mutant of the M pro bound to its endogenous N and C-terminal residues during dimeric association stage of the maturation process. We suggest this form is a transitional state during the C-terminal trans-cleavage. This data sheds light in the structural modifications of the SARS-CoV-2 main protease during its self-maturation process.


  • Organizational Affiliation

    Institute of Physics of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, Sao Carlos 13563-120, Brazil. Electronic address: andregodoy@ifsc.usp.br.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
309Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R9V (Subject of Investigation/LOI)
Query on R9V

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B]
(3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol
C14 H19 N O
HCBGIBWAPOFRKI-WDNDVIMCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.389α = 90
b = 101.679β = 90
c = 101.916γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2013/07600-3

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2021-07-28
    Changes: Database references
  • Version 1.3: 2023-07-26
    Changes: Data collection, Database references
  • Version 1.4: 2023-10-18
    Changes: Data collection, Refinement description