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- PDB-5bvj: The molecular mode of action and species specificity of canakinum... -

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Basic information

Entry
Database: PDB / ID: 5bvj
TitleThe molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta
Components
  • canakinumab Fab heavy-chain
  • canakinumab Fab light-chain
KeywordsIMMUNE SYSTEM / immunoglobulin / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRondeau, J.M.
CitationJournal: Mabs / Year: 2015
Title: The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1 beta.
Authors: Rondeau, J.M. / Ramage, P. / Zurini, M. / Gram, H.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 2.0Mar 11, 2020Group: Atomic model / Data collection / Polymer sequence
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / entity_poly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: canakinumab Fab light-chain
B: canakinumab Fab heavy-chain
C: canakinumab Fab light-chain
D: canakinumab Fab heavy-chain
E: canakinumab Fab light-chain
F: canakinumab Fab heavy-chain
G: canakinumab Fab light-chain
H: canakinumab Fab heavy-chain


Theoretical massNumber of molelcules
Total (without water)190,2448
Polymers190,2448
Non-polymers00
Water22,2311234
1
A: canakinumab Fab light-chain
B: canakinumab Fab heavy-chain


Theoretical massNumber of molelcules
Total (without water)47,5612
Polymers47,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-32 kcal/mol
Surface area19890 Å2
MethodPISA
2
C: canakinumab Fab light-chain
D: canakinumab Fab heavy-chain


Theoretical massNumber of molelcules
Total (without water)47,5612
Polymers47,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-33 kcal/mol
Surface area19290 Å2
MethodPISA
3
E: canakinumab Fab light-chain
F: canakinumab Fab heavy-chain


Theoretical massNumber of molelcules
Total (without water)47,5612
Polymers47,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-30 kcal/mol
Surface area19430 Å2
MethodPISA
4
G: canakinumab Fab light-chain
H: canakinumab Fab heavy-chain


Theoretical massNumber of molelcules
Total (without water)47,5612
Polymers47,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-30 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.621, 142.264, 83.802
Angle α, β, γ (deg.)90.000, 115.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
canakinumab Fab light-chain / ILARIS Fab / canakinumab Fab


Mass: 23381.908 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): myeloma / Cell line (production host): SP2/0 / Production host: Mus musculus (house mouse)
#2: Antibody
canakinumab Fab heavy-chain / ILARIS Fab / canakinumab Fab


Mass: 24179.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SP2/0 / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1234 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 12% PEG MME 5000, 50mM sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 114298 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.057 / Χ2: 0.952 / Net I/av σ(I): 27.517 / Net I/σ(I): 11.7 / Num. measured all: 552811
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.074.50.148113970.57199.9
2.07-2.154.90.112113680.509100
2.15-2.254.90.097114360.514100
2.25-2.374.90.086114090.521100
2.37-2.524.90.079114130.65100
2.52-2.714.90.069114100.806100
2.71-2.994.90.063114371.077100
2.99-3.424.90.054114061.478100
3.42-4.314.80.046114771.7399.9
4.31-1004.80.045115451.64899.6

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Processing

Software
NameVersionClassification
DENZO1.97.9data reduction
SCALEPACKdata scaling
CNSCNX2002refinement
PDB_EXTRACT3.15data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 25643448 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5760 5 %RANDOM
Rwork0.186 ---
obs-114268 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7882 Å2 / ksol: 0.3406 e/Å3
Displacement parametersBiso max: 74.84 Å2 / Biso mean: 25 Å2 / Biso min: 6.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-4.81 Å2
2---3.13 Å20 Å2
3---1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.1 Å
Refinement stepCycle: final / Resolution: 2→50.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13207 0 0 1234 14441
Biso mean---32.23 -
Num. residues----1732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.871.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it3.052
X-RAY DIFFRACTIONc_scangle_it4.282.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 960 5.1 %
Rwork0.194 17875 -
all-18835 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_pca.paramprotein_pca.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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