Download MendeleyPotent cross-reactive mAbs from BA.4/5 breakthrough infection
Stuart, D.I.To be published.
8CMA
SARS-CoV-2 Delta-RBD complexed with BA.4/5-35 Fab
- PDB DOI: https://doi.org/10.2210/pdb8CMA/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
- Expression System: Homo sapiens
- Mutation(s): Yes
- Deposited: 2023-02-18 Released: 2024-02-28
- Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS), Medical Research Council (MRC, United Kingdom)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.29 Å
- R-Value Free: 0.268
- R-Value Work: 0.231
- R-Value Observed: 0.233
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| BA.4/5-35 heavy chain | A [auth H] | 223 | 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: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike protein S1 | B [auth E] | 202 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 2 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: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| BA.4/5-35 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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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | D [auth E] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.29 Å
- R-Value Free: 0.268
- R-Value Work: 0.231
- R-Value Observed: 0.233
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 195.782 | α = 90 |
| b = 85.119 | β = 102.03 |
| c = 56.974 | γ = 90 |
| Software Name | Purpose |
|---|---|
| GDA | data collection |
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-02-28 Deposition Author(s): Zhou, D., Ren, J., Stuart, D.I.
| Funding Organization | Location | Grant Number |
|---|---|---|
| CAMS Innovation Fund for Medical Sciences (CIFMS) | United Kingdom | 2018-I2M-2-002 |
| Medical Research Council (MRC, United Kingdom) | United Kingdom | MR/N00065X/1 |
Revision History (Full details and data files)
- Version 1.0: 2024-02-28
Type: Initial release
