5TZT
Crystal structure of human CD47 ECD bound to Fab of C47B161
- PDB DOI: https://doi.org/10.2210/pdb5TZT/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2016-11-22 Released: 2017-03-15 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.89 Å
- R-Value Free: 0.328 
- R-Value Work: 0.257 
- R-Value Observed: 0.261 
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 |
Light Chain of Fab C47B161 | A [auth B], C [auth L] | 219 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Heavy Chain of Fab C47B161 | B [auth A], D [auth H] | 226 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Leukocyte surface antigen CD47 | E [auth C], F [auth D] | 129 | Homo sapiens | Mutation(s): 1  Gene Names: CD47, MER6 | |
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 | L [auth C], M [auth D], N [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | G [auth B], H [auth A], I [auth L], J [auth H], K [auth H] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PCA Query on PCA | B [auth A], D [auth H] | L-PEPTIDE LINKING | C5 H7 N O3 | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.89 Å
- R-Value Free: 0.328 
- R-Value Work: 0.257 
- R-Value Observed: 0.261 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 74.569 | α = 90 |
b = 60.974 | β = 90.05 |
c = 124.133 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data reduction |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2017-03-15  Deposition Author(s): Cardoso, R.M.F.
Revision History (Full details and data files)
- Version 1.0: 2017-03-15
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Polymer sequence, Structure summary - Version 2.1: 2021-03-24
Changes: Source and taxonomy, Structure summary - Version 2.2: 2023-10-04
Changes: Data collection, Database references, Refinement description