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- PDB-4kq3: Crystal structure of Anti-IL-17A antibody CNTO3186 -

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Basic information

Entry
Database: PDB / ID: 4kq3
TitleCrystal structure of Anti-IL-17A antibody CNTO3186
Components
  • CNTO3186 heavy chain
  • CNTO3186 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: Structural evidence for a constrained conformation of short CDR-L3 in antibodies.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Gilliland, G.L.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 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
L: CNTO3186 light chain
H: CNTO3186 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9577
Polymers47,4242
Non-polymers5345
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-17 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.450, 60.560, 72.140
Angle α, β, γ (deg.)90.00, 99.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody CNTO3186 light chain


Mass: 23234.652 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#2: Antibody CNTO3186 heavy chain


Mass: 24188.924 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293E / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 344 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG3000, 0.2 M ammonium acetate, 0.1 M MES, pH 6.5, cryoprotectant: 20% PEG3000, 0.16 M ammonium acetate, 0.1 M MES, PH 6.5, 24% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 4, 2008 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. all: 28013 / Num. obs: 28013 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 32.8
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.6 / % possible all: 55

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERSEARCH MODEL: 1RZ7 (VL)phasing
2CMR(VH)model building
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
2CMR(VH)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.472 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.16 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22523 997 3.6 %RANDOM
Rwork0.17063 ---
all0.17251 26958 --
obs0.17251 26958 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.36 Å2
2---0.35 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.92→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 34 339 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223363
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.9564575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79824.609128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67215530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3651511
X-RAY DIFFRACTIONr_chiral_restr0.0640.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212510
X-RAY DIFFRACTIONr_mcbond_it1.23922135
X-RAY DIFFRACTIONr_mcangle_it2.52843465
X-RAY DIFFRACTIONr_scbond_it15.413881228
X-RAY DIFFRACTIONr_scangle_it18.54881109
LS refinement shellResolution: 1.92→1.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 38 -
Rwork0.211 1164 -
obs--55 %

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