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- PDB-3e2m: LFA-1 I domain bound to inhibitors -

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Basic information

Entry
Database: PDB / ID: 3e2m
TitleLFA-1 I domain bound to inhibitors
ComponentsIntegrin alpha-L
KeywordsCELL ADHESION / INTEGRIN I-DOMAIN / LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1 / ALTERNATIVE SPLICING / CALCIUM / GLYCOPROTEIN / MAGNESIUM / MEMBRANE / POLYMORPHISM / RECEPTOR / TRANSMEMBRANE
Function / homology
Function and homology information


memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / Integrin cell surface interactions / phagocytosis / specific granule membrane / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. ...Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E2M / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSilvian, L.F.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Structure-activity relationship of ortho- and meta-phenol based LFA-1 ICAM inhibitors
Authors: Lin, E.Y. / Guckian, K.M. / Silvian, L. / Chin, D. / Boriack-Sjodin, P.A. / van Vlijmen, H. / Friedman, J.E. / Scott, D.M.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-L
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4244
Polymers42,1882
Non-polymers1,2352
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-7.3 kcal/mol
Surface area16490 Å2
MethodPISA
2
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7122
Polymers21,0941
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7122
Polymers21,0941
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.062, 69.608, 72.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-446-

HOH

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Components

#1: Protein Integrin alpha-L / Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule ...Leukocyte adhesion glycoprotein LFA-1 alpha chain / LFA-1A / Leukocyte function-associated molecule 1 alpha chain / CD11a antigen


Mass: 21094.172 Da / Num. of mol.: 2 / Fragment: VWFA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#2: Chemical ChemComp-E2M / cis-4-{[2-({4-[(1E)-3-morpholin-4-yl-3-oxoprop-1-en-1-yl]-2,3-bis(trifluoromethyl)phenyl}sulfanyl)phenoxy]methyl}cyclohexanecarboxylic acid


Mass: 617.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H29F6NO5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growpH: 4.5
Details: 5% PEG400, 20% PEG3350, 50MM K2HPO4 PH 4.5, 10MM MGCL2, 1MM INHIBITOR, pH 4.50, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 7, 2003 / Details: Blue confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. obs: 34005 / Rmerge(I) obs: 0.107

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LFA

1lfa


Resolution: 2→32.43 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.661 / SU ML: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.287 1196 5.1 %
Rwork0.215 --
obs0.219 23427 91.1 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2→32.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 84 368 3390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223088
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9944170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37125.294136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19315562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.978156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022264
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21687
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22116
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.51869
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95522946
X-RAY DIFFRACTIONr_scbond_it2.33131383
X-RAY DIFFRACTIONr_scangle_it2.4494.51224
X-RAY DIFFRACTIONr_rigid_bond_restr2.29833252
X-RAY DIFFRACTIONr_sphericity_free3.3243392
X-RAY DIFFRACTIONr_sphericity_bonded1.49333022
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.364 101 -
Rwork0.224 1683 -
obs--95.15 %

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