2AJF
Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor
- PDB DOI: https://doi.org/10.2210/pdb2AJF/pdb
- Classification: hydrolase/viral protein
- Organism(s): Homo sapiens, Severe acute respiratory syndrome-related coronavirus
- Expression System: Spodoptera frugiperda
- Mutation(s): No
- Deposited: 2005-08-01 Released: 2005-09-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.275
- R-Value Work: 0.218
- R-Value Observed: 0.221
This is version 2.1 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 |
| Angiotensin-converting enzyme-Related Carboxypeptidase (Ace2) | 597 | Homo sapiens | Mutation(s): 0 Gene Names: ACE2 EC: 3.4.17 |
 |
|
UniProt & NIH Common Fund Data Resources |
|||||
|
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1
Go to UniProtKB: Q9BYF1
|
|||||
|
PHAROS: Q9BYF1
GTEx: ENSG00000130234
|
|||||
Entity Groups |
|||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9BYF1 | ||||
Sequence AnnotationsExpand |
|||||
|
|||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 |
|||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| SARS-coronavirus spike protein | C [auth E], D [auth F] |
180 | Severe acute respiratory syndrome-related coronavirus | Mutation(s): 0 Gene Names: S |
 |
UniProt |
|||||
|
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus)
Explore P59594
Go to UniProtKB: P59594
|
|||||
Entity Groups |
|||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P59594 | ||||
Sequence AnnotationsExpand |
|||||
|
|||||
Oligosaccharides
Entity ID: 3 |
|||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E [auth C], F [auth D] |
3 |  |
N-Glycosylation | |
Glycosylation Resources |
|||||
|
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
|
|||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG |
G [auth A]
H [auth A] I [auth A] L [auth B] O [auth E] |
2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
 |
||
| ZN Query on ZN |
J [auth A], M [auth B] |
ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |
 |
||
| CL Query on CL |
K [auth A], N [auth B] |
CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
 |
||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.275
- R-Value Work: 0.218
- R-Value Observed: 0.221
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 82.299 | α = 90 |
| b = 119.429 | β = 91.97 |
| c = 113.237 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- Released Date: 2005-09-20 Deposition Author(s): Li, F., Li, W., Farzan, M., Harrison, S.C.
Revision History (Full details and data files)
- Version 1.0: 2005-09-20
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary
