7KFX
Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab)
- PDB DOI: https://doi.org/10.2210/pdb7KFX/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: 2.23 Å
- R-Value Free: 0.226
- R-Value Work: 0.191
- R-Value Observed: 0.193
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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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| heavy chain of human antibody C1A-C2 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-C2 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: 2.23 Å
- R-Value Free: 0.226
- R-Value Work: 0.191
- R-Value Observed: 0.193
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 83.455 | α = 90 |
| b = 149.192 | β = 90 |
| c = 146.143 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| PHENIX | data processing |
| O | model building |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | 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
