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- PDB-4qxg: Antigen binding fragment of an anti IFNAR1 antibody -

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Basic information

Entry
Database: PDB / ID: 4qxg
TitleAntigen binding fragment of an anti IFNAR1 antibody
Components
  • Fab, heavy chain, IgG1
  • Fab, light chain, IgG1
KeywordsIMMUNE SYSTEM / IgV and IgC type folds / antigen binding / IFNAR1 / interferon alpha receptor 1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOganesyan, V.Y. / Dall'Acqua, W.F.
CitationJournal: MAbs / Year: 2015
Title: Molecular basis for antagonistic activity of anifrolumab, an anti-interferon-alpha receptor 1 antibody.
Authors: Peng, L. / Oganesyan, V. / Wu, H. / Dall'Acqua, W.F. / Damschroder, M.M.
History
DepositionJul 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
H: Fab, heavy chain, IgG1
L: Fab, light chain, IgG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2445
Polymers47,0182
Non-polymers2263
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-30 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.456, 57.286, 100.212
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab, heavy chain, IgG1


Mass: 23571.545 Da / Num. of mol.: 1 / Fragment: Fab, heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab, light chain, IgG1


Mass: 23445.965 Da / Num. of mol.: 1 / Fragment: Fab, light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 192 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM potassium di-hydrogen phosphate, 100 mM MES, pH 6.5 and 20% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 10, 2007
RadiationMonochromator: VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.17→48 Å / Num. all: 22461 / Num. obs: 21383 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 27 Å2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0117refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.015 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24901 985 5.2 %RANDOM
Rwork0.1903 ---
all0.1933 22461 --
obs0.1933 18074 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å2-0.32 Å2
2---1.2 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 12 189 3487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023375
X-RAY DIFFRACTIONr_bond_other_d0.0010.022278
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.964589
X-RAY DIFFRACTIONr_angle_other_deg0.723.0035565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7915430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80124.077130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79815544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9771515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 75 -
Rwork0.236 1250 -
obs--98.59 %

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