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 
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 
wwPDB Validation   3D Report Full Report
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike glycoprotein | 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 Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0DTC2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
IgG heavy chain | B [auth H] | 458 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
IgG light chain | C [auth L] | 216 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 | 3D Interactions | |
EDO Query on EDO | F [auth L], G [auth L] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
NI Query on 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 Name | Purpose |
---|---|
Coot | refinement |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |
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 (Full details and data files)
- 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