5LGK
Crystal structure of the human IgE-Fc bound to its B cell receptor derCD23
- PDB DOI: https://doi.org/10.2210/pdb5LGK/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Expression System: Mus musculus, Escherichia coli
- Mutation(s): No 
- Deposited: 2016-07-07 Released: 2017-04-05 
- Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust, Asthma UK
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.50 Å
- R-Value Free: 0.278 
- R-Value Work: 0.266 
- R-Value Observed: 0.267 
wwPDB Validation   3D Report Full Report
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 |
Ig epsilon chain C region | 307 | Homo sapiens | Mutation(s): 0  Gene Names: IGHE | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01854 (Homo sapiens) Explore P01854  Go to UniProtKB:  P01854 | |||||
PHAROS:  P01854 GTEx:  ENSG00000211891  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P01854 | ||||
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 |
Low affinity immunoglobulin epsilon Fc receptor | 120 | Homo sapiens | Mutation(s): 0  Gene Names: FCER2, CD23A, CLEC4J, FCE2, IGEBF | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06734 (Homo sapiens) Explore P06734  Go to UniProtKB:  P06734 | |||||
PHAROS:  P06734 GTEx:  ENSG00000104921  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06734 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth A], J [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.50 Å
- R-Value Free: 0.278 
- R-Value Work: 0.266 
- R-Value Observed: 0.267 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 80.52 | α = 117.87 |
b = 85.32 | β = 90.32 |
c = 88.23 | γ = 112.62 |
Software Name | Purpose |
---|---|
Aimless | data scaling |
PHASER | phasing |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-04-05  Deposition Author(s): Dhaliwal, B., Pang, M.O.Y., Sutton, B.J.
Funding Organization | Location | Grant Number |
---|---|---|
Medical Research Council (United Kingdom) | United Kingdom | -- |
Wellcome Trust | United Kingdom | -- |
Asthma UK | United Kingdom | -- |
Revision History (Full details and data files)
- Version 1.0: 2017-04-05
Type: Initial release - Version 1.1: 2017-04-12
Changes: Database references - Version 1.2: 2017-09-13
Changes: Advisory, Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary