7S4S
Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex CoV11 Fab
- PDB DOI: https://doi.org/10.2210/pdb7S4S/pdb
- Classification: VIRAL PROTEIN/Immune System
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2021-09-09 Released: 2021-09-22
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.198
- R-Value Work: 0.166
- R-Value Observed: 0.167
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 protein S1 | 231 | 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 |
| CoV11 heavy chain | B [auth H] | 221 | 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 |
| CoV11 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 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 |  | ||
| SO4 Query on SO4 | E [auth A], G [auth H], I [auth L], J [auth L], K [auth L] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ACT Query on ACT | F [auth A], H, L, M [auth L] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.198
- R-Value Work: 0.166
- R-Value Observed: 0.167
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.056 | α = 90 |
| b = 111.259 | β = 90 |
| c = 142.948 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-09-22 Deposition Author(s): Tolbert, W.D., Pazgier, M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01 AI116274 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | P01 AI120756 |
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | R01 AI129769 |
Revision History (Full details and data files)
- Version 1.0: 2021-09-22
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Refinement description - Version 1.2: 2023-11-15
Changes: Database references
