1MQ8

Crystal structure of alphaL I domain in complex with ICAM-1

• PDB DOI: https://doi.org/10.2210/pdb1MQ8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-09-15 Released: 2003-01-14 
• Deposition Author(s): Shimaoka, M., Xiao, T., Liu, J.-H., Yang, Y., Dong, Y., Jun, C.-D., McCormack, A., Zhang, R., Joachimiak, A., Takagi, J., Wang, J.-H., Springer, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.313 
• R-Value Work: 0.264 
• R-Value Observed: 0.280 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.26 kDa 
• Atom Count: 5,854 
• Modelled Residue Count: 722 
• Deposited Residue Count: 936 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
intercellular adhesion molecule-1	A, C	291	Homo sapiens	Mutation(s): 0  Gene Names: ICAM-1
UniProt & NIH Common Fund Data Resources
Find proteins for P05362 (Homo sapiens) Explore P05362  Go to UniProtKB:  P05362
PHAROS:  P05362 GTEx:  ENSG00000090339

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	B, D	177	Homo sapiens	Mutation(s): 2  Gene Names: LFA-1 (AlphaLbeta2)
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens) Explore P20701  Go to UniProtKB:  P20701
PHAROS:  P20701 GTEx:  ENSG00000005844

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], L [auth C], M [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	K [auth B], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.313 
• R-Value Work: 0.264 
• R-Value Observed: 0.280 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.56	α = 95.39
b = 62.868	β = 106.67
c = 81.517	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-14 
Deposition Author(s): Shimaoka, M., Xiao, T., Liu, J.-H., Yang, Y., Dong, Y., Jun, C.-D., McCormack, A., Zhang, R., Joachimiak, A., Takagi, J., Wang, J.-H., Springer, T.A.

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-27
  Changes: Database references, Structure summary