7KC6 | pdb_00007kc6

X-ray structure of Lfa-1 I domain in complex with Lovastatin collected at 273 K

• PDB DOI: https://doi.org/10.2210/pdb7KC6/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-10-05 Released: 2021-10-06 
• Deposition Author(s): Woldeyes, R.A., Hallenbeck, K.K., Pfaff, S.J., Lee, G., Cortez, S.V., Kelly, M.J., Akassoglou, K., Arkin, M.R., Fraser, J.S.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Divergent conformational dynamics controls allosteric ligand accessibility across evolutionarily related I-domain-containing integrins

Woldeyes, R.A., Hallenbeck, K.K., Pfaff, S.J., Lee, G., Cortez, S.V., Kelly, M.J., Akassoglou, K., Arkin, M.R., Fraser, J.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.73 kDa 
• Atom Count: 3,458 
• Modeled Residue Count: 368 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	A [auth C], B [auth A]	184	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
803 (Subject of Investigation/LOI)	C, E [auth A]	LOVASTATIN C24 H36 O5 PCZOHLXUXFIOCF-BXMDZJJMSA-N
MG	D [auth C], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
803	BindingDB:  7KC6	Kd: 1.29e+4 (nM) from 1 assay(s)
		IC50: 2400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.889	α = 90
b = 46.078	β = 104.606
c = 127.233	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Woldeyes, R.A., Hallenbeck, K.K., Pfaff, S.J., Lee, G., Cortez, S.V., Kelly, M.J., Akassoglou, K., Arkin, M.R., Fraser, J.S.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	GRFP
National Science Foundation (NSF, United States)	United States	STC-1231306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM110580

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description