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- PDB-1xuo: X-ray structure of LFA-1 I-domain bound to a 1,4-diazepane-2,5-di... -

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Basic information

Entry
Database: PDB / ID: 1xuo
TitleX-ray structure of LFA-1 I-domain bound to a 1,4-diazepane-2,5-dione inhibitor at 1.8A resolution
ComponentsIntegrin alpha-L
KeywordsIMMUNE SYSTEM / I-domain / Integrin
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 / heterophilic cell-cell adhesion / integrin complex / 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 / heterophilic cell-cell adhesion / integrin complex / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / receptor clustering / phagocytosis / Integrin cell surface interactions / specific granule membrane / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 ...Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / 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-LA1 / Integrin alpha-L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWattanasin, S. / Kallen, J. / Myers, S. / Guo, Q. / Sabio, M. / Ehrhardt, C. / Albert, R. / Hommel, U. / Weckbecker, G. / Welzenbach, K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: 1,4-Diazepane-2,5-diones as novel inhibitors of LFA-1
Authors: Wattanasin, S. / Kallen, J. / Myers, S. / Guo, Q. / Sabio, M. / Ehrhardt, C. / Albert, R. / Hommel, U. / Weckbecker, G. / Welzenbach, K. / Weitz-Schmidt, G.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 20, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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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)43,4365
Polymers42,8512
Non-polymers5853
Water4,432246
1
A: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9873
Polymers21,4261
Non-polymers5612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integrin alpha-L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4502
Polymers21,4261
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.259, 59.995, 142.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is chain A (or chain B)

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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


Mass: 21425.561 Da / Num. of mol.: 2 / Fragment: I-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20701
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Details: C33H36N4O3
#3: Chemical ChemComp-LA1 / (2R)-2-[3-ISOBUTYL-2,5-DIOXO-4-(QUINOLIN-3-YLMETHYL)-1,4-DIAZEPAN-1-YL]-N-METHYL-3-(2-NAPHTHYL)PROPANAMIDE / (S)-2-((S)-3-ISOBUTYL-2,5-DIOXO-4-QUINOLIN-3-YLMETHYL-[1,4]DIAZEPAN-1YL)-N-METHYL-3-NAPHTALEN-2-YL-PROPIONAMIDE


Mass: 536.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H36N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.4 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. all: 35097 / Num. obs: 35097 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.067 / Net I/σ(I): 29.4
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 4.3 / Num. unique all: 3631 / Rsym value: 0.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CQP

1cqp


Resolution: 1.8→8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.374 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21409 1844 5 %RANDOM
Rwork0.18353 ---
obs0.18505 35097 99.73 %-
all-35097 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.754 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.75 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 42 246 3154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222969
X-RAY DIFFRACTIONr_bond_other_d0.0010.022681
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9654001
X-RAY DIFFRACTIONr_angle_other_deg0.77336275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88925.299134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22715544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.618156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
X-RAY DIFFRACTIONr_nbd_refined0.2050.2526
X-RAY DIFFRACTIONr_nbd_other0.1720.22479
X-RAY DIFFRACTIONr_nbtor_other0.0860.21522
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.213
X-RAY DIFFRACTIONr_mcbond_it1.2461.52292
X-RAY DIFFRACTIONr_mcbond_other0.1871.5724
X-RAY DIFFRACTIONr_mcangle_it1.39122864
X-RAY DIFFRACTIONr_scbond_it2.2131451
X-RAY DIFFRACTIONr_scangle_it3.124.51137
LS refinement shellResolution: 1.802→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 108
Rwork0.212 2452

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