6ZLR

Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex-An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface.

Nichols, C.Ng, J.Keshu, A.Fraternali, F.De Nicola, G.F.

(2020) Front Pharmacol 11: 615211-615211

  • DOI: https://doi.org/10.3389/fphar.2020.615211
  • Primary Citation of Related Structures:  
    6ZLR

  • PubMed Abstract: 

    In-crystal fragment screening is a powerful tool to chemically probe the surfaces used by proteins to interact, and identify the chemical space worth exploring to design protein-protein inhibitors. A crucial prerequisite is the identification of a crystal form where the target area is exposed and accessible to be probed by fragments. Here we report a crystal form of the SARS-CoV-2 Receptor Binding Domain in complex with the CR3022 antibody where the ACE2 binding site on the Receptor Binding Domain is exposed and accessible. This crystal form of the complex is a valuable tool to develop antiviral molecules that could act by blocking the virus entry in cells.


  • Organizational Affiliation

    British Heart Foundation Centre of Excellence, Department of Cardiology, Rayne Institute, St Thomas' Hospital, King's College London, London, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth EEE],
D [auth AAA],
G [auth DDD]
231Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CR3022 FAB HEAVY CHAINB [auth HHH],
E [auth BBB],
H [auth FFF]
222Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CR3022 FAB LIGHT CHAINC [auth LLL],
F [auth CCC],
I [auth GGG]
221Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.13α = 90
b = 207.13β = 90
c = 199.866γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary