7CM4

Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59

• PDB DOI: https://doi.org/10.2210/pdb7CM4/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Spodoptera frugiperda, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2020-07-24 Released: 2021-01-20 
• Deposition Author(s): Kim, Y.G., Jeong, J.H., Bae, J.S., Lee, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.242 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 99.97 kDa 
• Atom Count: 4,985 
• Modelled Residue Count: 635 
• Deposited Residue Count: 900 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	226	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
IgG heavy chain	B [auth H]	458	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG light chain	C [auth L]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G17392HI GlyCosmos:  G17392HI GlyGen:  G17392HI

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth L], G [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	E [auth H], H [auth L]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 0.242 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.55	α = 90
b = 167.6	β = 90
c = 169.05	γ = 90

Software Package:

Software Name	Purpose
Coot	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-20 
Deposition Author(s): Kim, Y.G., Jeong, J.H., Bae, J.S., Lee, J.

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description