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- PDB-2o7n: CD11A (LFA1) I-domain complexed with 7A-[(4-cyanophenyl)methyl]-6... -

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Basic information

Entry
Database: PDB / ID: 2o7n
TitleCD11A (LFA1) I-domain complexed with 7A-[(4-cyanophenyl)methyl]-6-(3,5-dichlorophenyl)-5-oxo-2,3,5,7A-tetrahydro-1H-pyrrolo[1,2-A]pyrrole-7-carbonitrile
ComponentsIntegrin alpha-L
KeywordsCELL ADHESION / INHIBITOR / PROTEIN-LIGAND COMPLEX
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 / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / 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 / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / 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 / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / 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 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / 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-2O7 / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSheriff, S.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Design of LFA-1 antagonists based on a 2,3-dihydro-1H-pyrrolizin-5(7aH)-one scaffold.
Authors: Dodd, D.S. / Sheriff, S. / Chang, C.J. / Stetsko, D.K. / Phillips, L.M. / Zhang, Y. / Launay, M. / Potin, D. / Vaccaro, W. / Poss, M.A. / McKinnon, M. / Barrish, J.C. / Suchard, S.J. / Murali Dhar, T.G.
#1: Journal: J.Med.Chem. / Year: 2006
Title: Discovery and development of 5-[(5S,9R)-9- (4-cyanophenyl)-3-(3,5-dichlorophenyl)-1- methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non- 7-yl-methyl]-3-thiophenecarboxylic acid (BMS-587101)--a small ...Title: Discovery and development of 5-[(5S,9R)-9- (4-cyanophenyl)-3-(3,5-dichlorophenyl)-1- methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non- 7-yl-methyl]-3-thiophenecarboxylic acid (BMS-587101)--a small molecule antagonist leukocyte function associated antigen-1.
Authors: Potin, D. / Launay, M. / Monatlik, F. / Malabre, P. / Fabreguettes, M. / Fouquet, A. / Maillet, M. / Nicolai, E. / Dorgeret, L. / Chevallier, F. / Besse, D. / Dufort, M. / Caussade, F. / ...Authors: Potin, D. / Launay, M. / Monatlik, F. / Malabre, P. / Fabreguettes, M. / Fouquet, A. / Maillet, M. / Nicolai, E. / Dorgeret, L. / Chevallier, F. / Besse, D. / Dufort, M. / Caussade, F. / Ahmad, S.Z. / Stetsko, D.K. / Skala, S. / Davis, P.M. / Balimane, P. / Patel, K. / Yang, Z. / Marathe, P. / Postelneck, J. / Townsend, R.M. / Goldfarb, V. / Sheriff, S. / Einspahr, H. / Kish, K. / Malley, M.F. / DiMarco, J.D. / Gougoutas, J.Z. / Kadiyala, P. / Cheney, D.L. / Tejwani, R.W. / Murphy, D.K. / Mcintyre, K.W. / Yang, X. / Chao, S. / Leith, L. / Xiao, Z. / Mathur, A. / Chen, B.C. / Wu, D.R. / Traeger, S.C. / McKinnon, M. / Barrish, J.C. / Robl, J.A. / Iwanowicz, E.J. / Suchard, S.J. / Dhar, T.G.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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

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Assembly

Deposited unit
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3442
Polymers20,9361
Non-polymers4081
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.600, 88.400, 71.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-348-

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: 20935.980 Da / Num. of mol.: 1 / Fragment: VWFA DOMAIN, RESIDUES 154-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: MINIMAL MEDIA / Gene: ITGAL, CD11A / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20701
#2: Chemical ChemComp-2O7 / 7A-[(4-cyanophenyl)methyl]-6-(3,5-dichlorophenyl)-5-oxo-2,3,5,7A-tetrahydro-1H-pyrrolo[1,2-A]pyrrole-7-carbonitrile / (7aS)-7a-(4-cyanobenzyl)-6-(3,5-dichlorophenyl)-5-oxo-2,3,5,7a-tetrahydro-1H-pyrrolizine-7-carbonitrile


Mass: 408.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H15Cl2N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / pH: 8.9
Details: 78% (W/V) SODIUM CITRATE, 3% (V/V) ETHYLENE GLYCOL, 0.1 M SODIUM CITRATE, PH 5.6 (FINAL PH 8.9), VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.90

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 21828 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.9 / % possible all: 96.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
AMoREphasing
CNX2000.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LFA

1lfa


Resolution: 1.75→35.55 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1680683.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 643 3 %RANDOM
Rwork0.215 ---
obs0.215 21758 99.4 %-
all-21758 --
Solvent computationSolvent model: BABINET / Bsol: 280 Å2 / ksol: 1 e/Å3
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2---3.05 Å20 Å2
3---4.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 28 122 1609
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 1.75→1.83 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.279 74 2.8 %
Rwork0.261 2542 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION42O7.PAR2O7.TOP

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