2JJT
Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha
- PDB DOI: https://doi.org/10.2210/pdb2JJT/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: 2.30 Å
- R-Value Free: 0.288
- R-Value Work: 0.235
- R-Value Observed: 0.238
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 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | E [auth C] F [auth C] G [auth C] H [auth D] I [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| 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: 2.30 Å
- R-Value Free: 0.288
- R-Value Work: 0.235
- R-Value Observed: 0.238
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.62 | α = 90 |
| b = 63.72 | β = 90 |
| c = 123.02 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | 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
