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- PDB-1cqp: CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX LFA-1 (CD11A) I-DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1cqp
TitleCRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX LFA-1 (CD11A) I-DOMAIN / LOVASTATIN AT 2.6 A RESOLUTION
ComponentsANTIGEN CD11A (P180)
KeywordsIMMUNE SYSTEM / ROSSMANN FOLD / STRUCTURAL BASIS FOR LFA-1 INHIBITION
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
LOVASTATIN / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsKallen, J. / Welzenbach, K. / Ramage, P. / Geyl, D. / Kriwacki, R. / Legge, G. / Cottens, S. / Weitz-Schmidt, G. / Hommel, U.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structural basis for LFA-1 inhibition upon lovastatin binding to the CD11a I-domain.
Authors: Kallen, J. / Welzenbach, K. / Ramage, P. / Geyl, D. / Kriwacki, R. / Legge, G. / Cottens, S. / Weitz-Schmidt, G. / Hommel, U.
History
DepositionAug 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ANTIGEN CD11A (P180)
B: ANTIGEN CD11A (P180)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4996
Polymers41,6422
Non-polymers8584
Water1,54986
1
A: ANTIGEN CD11A (P180)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2503
Polymers20,8211
Non-polymers4292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTIGEN CD11A (P180)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2503
Polymers20,8211
Non-polymers4292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.700, 77.700, 91.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein ANTIGEN CD11A (P180) / INTEGRIN ALPHA L / LYMPHOCYTE FUNCTION-ASSOCIATED ANTIGEN 1 / ALPHA POLYPEPTIDE


Mass: 20820.859 Da / Num. of mol.: 2 / Fragment: I-DOMAIN, RESIDUES 153-334
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH LOVASTATIN WHICH OCCURS NATURALLY IN FUNGI
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P20701
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-803 / LOVASTATIN / MK-803 / LOVALIP / MEVACOR


Mass: 404.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H36O5 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, HEPES, MAGNESIUM SULFATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMHEPES1reservoir
230 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Feb 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 16457 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 13.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.484 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 87179
Reflection shell
*PLUS
% possible obs: 99.8 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.6→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1163 7.3 %RANDOM
Rwork0.19 ---
all0.19 15873 --
obs0.19 15873 99.9 %-
Displacement parametersBiso mean: 36.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 60 86 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.081.5
X-RAY DIFFRACTIONx_mcangle_it6.142
X-RAY DIFFRACTIONx_scbond_it6.682
X-RAY DIFFRACTIONx_scangle_it10.132.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 209 8.1 %
Rwork0.301 2358 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2GEN_X.PRMTOPH19.PEP
X-RAY DIFFRACTION3PARAM.MGTOPH19.H2O
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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