7U8E
Crystal structure of antibody Ab246 in complex with SARS-CoV-2 receptor binding domain
- PDB DOI: https://doi.org/10.2210/pdb7U8E/pdb
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2022-03-08 Released: 2023-03-15
- Funding Organization(s): Department of Defense (DOD, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.247
- R-Value Work: 0.204
- R-Value Observed: 0.206
This is version 1.4 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 | 205 | 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 |
| Antibody Ab246 Fab heavy chain | B [auth H] | 227 | 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 |
| Antibody Ab246 Fab light chain | C [auth L] | 221 | 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 3 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 |  | ||
| GOL Query on GOL | E [auth A] F [auth A] H I [auth H] J [auth L] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | G [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.247
- R-Value Work: 0.204
- R-Value Observed: 0.206
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 194.797 | α = 90 |
| b = 41.603 | β = 107.03 |
| c = 98.991 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-03-15 Deposition Author(s): Sankhala, R.S., Joyce, M.G.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Department of Defense (DOD, United States) | United States | W81XWH-18-2-0040 |
Revision History (Full details and data files)
- Version 1.0: 2023-03-15
Type: Initial release - Version 1.1: 2023-10-25
Changes: Data collection, Refinement description - Version 1.2: 2024-01-10
Changes: Database references - Version 1.3: 2024-01-17
Changes: Database references - Version 1.4: 2024-02-14
Changes: Database references
