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 | |||||
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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 | |||||
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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 | |||||
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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