6XKQ

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-250

• PDB DOI: https://doi.org/10.2210/pdb6XKQ/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Trichoplusia ni, Mus musculus
• Mutation(s): No 


• Deposited: 2020-06-26 Released: 2020-10-14 
• Deposition Author(s): Yuan, M., Liu, H., Zhu, X., Wu, N.C., Wilson, I.A.
• Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.255 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 73.37 kDa 
• Atom Count: 4,525 
• Modelled Residue Count: 583 
• Deposited Residue Count: 671 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	231	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CV07-250 Heavy Chain	B [auth H]	224	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CV07-250 Light Chain	C [auth L]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.255 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.97	α = 90
b = 80.07	β = 90
c = 153.685	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Yuan, M., Liu, H., Zhu, X., Wu, N.C., Wilson, I.A.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI139445

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2020-11-25
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description