2JJS
Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha
- PDB DOI: https://doi.org/10.2210/pdb2JJS/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): Yes 
- Deposited: 2008-04-22 Released: 2008-08-05 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.213 
- R-Value Work: 0.169 
- R-Value Observed: 0.171 
This is version 2.2 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 |
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1 | 126 | Homo sapiens | Mutation(s): 0  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P78324 (Homo sapiens) Explore P78324  Go to UniProtKB:  P78324 | |||||
PHAROS:  P78324 GTEx:  ENSG00000198053  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P78324 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
LEUKOCYTE SURFACE ANTIGEN CD47 | 127 | Homo sapiens | Mutation(s): 1  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q08722 (Homo sapiens) Explore Q08722  Go to UniProtKB:  Q08722 | |||||
PHAROS:  Q08722 GTEx:  ENSG00000196776  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q08722 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A] K [auth B] Q [auth C] R [auth C] W [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
IOD Query on IOD | AA [auth D] BA [auth D] F [auth A] G [auth A] H [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PCA Query on PCA | C, D | L-PEPTIDE LINKING | C5 H7 N O3 | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.213 
- R-Value Work: 0.169 
- R-Value Observed: 0.171 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 42.477 | α = 90 |
b = 72.41 | β = 95.01 |
c = 89.826 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2008-08-05  Deposition Author(s): Hatherley, D., Graham, S.C., Turner, J., Harlos, K., Stuart, D.I., Barclay, A.N.
Revision History (Full details and data files)
- Version 1.0: 2008-08-05
Type: Initial release - Version 1.1: 2011-05-07
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2019-03-13
Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other, Structure summary - Version 1.4: 2019-04-03
Changes: Data collection, Source and taxonomy - Version 2.0: 2020-03-11
Changes: Data collection, Other, Polymer sequence - Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 2.2: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary