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- PDB-1rd4: An allosteric inhibitor of LFA-1 bound to its I-domain -

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Basic information

Entry
Database: PDB / ID: 1rd4
TitleAn allosteric inhibitor of LFA-1 bound to its I-domain
ComponentsIntegrin alpha-L
KeywordsIMMUNE SYSTEM
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 / receptor clustering / leukocyte cell-cell adhesion ...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 / receptor clustering / leukocyte cell-cell adhesion / 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-L08 / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCrump, M.P. / Ceska, T.A. / Spyracopoulos, L. / Henry, A. / Archibald, S.C. / Alexander, R. / Taylor, R.J. / Findlow, S.C. / O'Connell, J. / Robinson, M.K. / Shock, A.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry
Authors: Crump, M.P. / Ceska, T.A. / Spyracopoulos, L. / Henry, A. / Archibald, S.C. / Alexander, R. / Taylor, R.J. / Findlow, S.C. / O'Connell, J. / Robinson, M.K. / Shock, A.
History
DepositionNov 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 23, 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 / 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
C: Integrin alpha-L
D: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5948
Polymers86,6804
Non-polymers1,9144
Water00
1
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1482
Polymers21,6701
Non-polymers4791
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1482
Polymers21,6701
Non-polymers4791
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1482
Polymers21,6701
Non-polymers4791
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1482
Polymers21,6701
Non-polymers4791
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.960, 64.410, 66.210
Angle α, β, γ (deg.)74.21, 90.00, 87.26
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 21669.896 Da / Num. of mol.: 4 / Fragment: I Domain, residues 125-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAL, CD11A / Production host: Escherichia coli (E. coli) / References: UniProt: P20701
#2: Chemical
ChemComp-L08 / 1-ACETYL-4-(4-{4-[(2-ETHOXYPHENYL)THIO]-3-NITROPHENYL}PYRIDIN-2-YL)PIPERAZINE


Mass: 478.563 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H26N4O4S

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growpH: 4.6
Details: 30% (w/v) PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 31, 2001 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 26155 / Num. obs: 26155 / % possible obs: 91.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LFA

1lfa


Resolution: 2.4→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 2615 Random
Rwork0.236 --
all0.245 26155 -
obs0.245 26155 -
Displacement parametersBiso mean: 14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 136 0 6052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.18

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