7C01
Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD
- PDB DOI: https://doi.org/10.2210/pdb7C01/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2020-04-29 Released: 2020-05-27 
- Funding Organization(s): Chinese Academy of Sciences, Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.88 Å
- R-Value Free: 0.265 
- R-Value Work: 0.218 
- R-Value Observed: 0.220 
This is version 1.5 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike protein S1 | A, D [auth B] | 229 | 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 | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CB6 heavy chain | B [auth H], E [auth C] | 233 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
CB6 light chain | C [auth L], F [auth D] | 217 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A], H [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.88 Å
- R-Value Free: 0.265 
- R-Value Work: 0.218 
- R-Value Observed: 0.220 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 87.4 | α = 90 |
b = 106.73 | β = 90 |
c = 170.59 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
Blu-Ice | data collection |
HKL-2000 | data reduction |
UCSD-system | data processing |
PHASER | phasing |
HKL-2000 | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-05-27  Deposition Author(s): Shi, R., Qi, J., Wang, Q., Gao, F.G., Yan, J.
Funding Organization | Location | Grant Number |
---|---|---|
Chinese Academy of Sciences | China | XDB29040201 |
Ministry of Science and Technology (MoST, China) | China | 2018ZX09711003 |
Ministry of Science and Technology (MoST, China) | China | 2020YFC0841400 |
National Natural Science Foundation of China (NSFC) | China | 81922044 |
Revision History (Full details and data files)
- Version 1.0: 2020-05-27
Type: Initial release - Version 1.1: 2020-06-10
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.3: 2020-08-19
Changes: Database references, Structure summary - Version 1.4: 2021-03-10
Changes: Structure summary - Version 1.5: 2023-11-29
Changes: Data collection, Database references, Refinement description