3BN3
crystal structure of ICAM-5 in complex with aL I domain
- PDB DOI: https://doi.org/10.2210/pdb3BN3/pdb
- Classification: Cell adhesion, immune system
- Organism(s): Homo sapiens
- Expression System: Escherichia coli, Cricetulus griseus
- Mutation(s): Yes 
- Deposited: 2007-12-13 Released: 2008-08-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.235 
- R-Value Work: 0.191 
- R-Value Observed: 0.193 
wwPDB Validation   3D Report Full Report
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 |
Integrin alpha-L | 180 | Homo sapiens | Mutation(s): 3  Gene Names: ITGAL, CD11A | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P20701 (Homo sapiens) Explore P20701  Go to UniProtKB:  P20701 | |||||
PHAROS:  P20701 GTEx:  ENSG00000005844  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P20701 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Intercellular adhesion molecule 5 | 196 | Homo sapiens | Mutation(s): 0  Gene Names: ICAM5, TLCN, TLN | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UMF0 (Homo sapiens) Explore Q9UMF0  Go to UniProtKB:  Q9UMF0 | |||||
PHAROS:  Q9UMF0 GTEx:  ENSG00000105376  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9UMF0 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth B], F [auth B], G [auth B], H [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | I [auth B], J [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
MG Query on MG | D [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.235 
- R-Value Work: 0.191 
- R-Value Observed: 0.193 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 61.793 | α = 90 |
b = 71.507 | β = 90 |
c = 143.871 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2008-08-19  Deposition Author(s): Zhang, H., Springer, T.A., Wang, J.-h.
Revision History (Full details and data files)
- Version 1.0: 2008-08-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2021-10-20
Changes: Database references, Structure summary - Version 2.2: 2023-08-30
Changes: Data collection, Refinement description