7KFY
Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-F10 Fab)
- PDB DOI: https://doi.org/10.2210/pdb7KFY/pdb
- Classification: IMMUNE SYSTEM/Viral protein
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2020-10-15 Released: 2020-12-02 
- Funding Organization(s): Other private
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.16 Å
- R-Value Free: 0.249 
- R-Value Work: 0.205 
- R-Value Observed: 0.208 
This is version 1.2 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 glycoprotein | 228 | 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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(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
heavy chain of human antibody C1A-F10 Fab | B [auth H] | 225 | 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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
light chain of human antibody C1A-F10 Fab | C [auth L] | 214 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.16 Å
- R-Value Free: 0.249 
- R-Value Work: 0.205 
- R-Value Observed: 0.208 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 85.74 | α = 90 |
b = 146.801 | β = 90 |
c = 144.593 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
PHENIX | data processing |
O | model building |
XDS | data reduction |
XDS | data scaling |
PARROT | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-12-02  Deposition Author(s): Pan, J., Abraham, J., Clark, L., Clark, S.
Funding Organization | Location | Grant Number |
---|---|---|
Other private | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2020-12-02
Type: Initial release - Version 1.1: 2021-01-20
Changes: Database references, Source and taxonomy, Structure summary - Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description