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- PDB-9sg2: Ixekizumab Fab in complex with human IL-17A -

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Basic information

Entry
Database: PDB / ID: 9sg2
TitleIxekizumab Fab in complex with human IL-17A
Components
  • Interleukin-17A
  • Ixekizumab Fab heavy-chain
  • Ixekizumab Fab light-chain
KeywordsCYTOKINE / Therapeutic antibody / Ixekizumab
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / intestinal epithelial structure maintenance / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-6 production / response to wounding / positive regulation of tumor necrosis factor production / cell-cell signaling / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / gene expression / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / innate immune response / external side of plasma membrane / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine-knot cytokine
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsRondeau, J.-M. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2025
Title: IL-17A complexes with therapeutic antibodies exhibit distinct size distributions, potentially contributing to clinically observed immunogenicity.
Authors: Ungan, D. / Be, C. / Baczyk, P. / Mittermeier, S. / Lehmann, S. / Wiesmann, C. / Huber, T. / Kolbinger, F. / Rondeau, J.M.
History
DepositionAug 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-17A
H: Ixekizumab Fab heavy-chain
L: Ixekizumab Fab light-chain


Theoretical massNumber of molelcules
Total (without water)64,8013
Polymers64,8013
Non-polymers00
Water00
1
A: Interleukin-17A
H: Ixekizumab Fab heavy-chain
L: Ixekizumab Fab light-chain

A: Interleukin-17A
H: Ixekizumab Fab heavy-chain
L: Ixekizumab Fab light-chain


Theoretical massNumber of molelcules
Total (without water)129,6016
Polymers129,6016
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area15690 Å2
ΔGint-105 kcal/mol
Surface area47220 Å2
Unit cell
Length a, b, c (Å)125.730, 125.730, 107.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Interleukin-17A / IL-17 / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 15712.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct included amino acids 20 to 155 of Uniprot entry Q16552 with a N-terminal His6 tag followed by a PreScission cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1 / References: UniProt: Q16552
#2: Antibody Ixekizumab Fab heavy-chain


Mass: 24958.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Ixekizumab Fab light-chain


Mass: 24129.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M TRIS pH 8.5, 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.92→88.91 Å / Num. obs: 19277 / % possible obs: 100 % / Redundancy: 12.55 % / CC1/2: 0.999 / Rrim(I) all: 0.163 / Net I/σ(I): 11.99
Reflection shellResolution: 2.92→3 Å / Redundancy: 13.35 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 1400 / CC1/2: 0.482 / Rrim(I) all: 2.972 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→81.72 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.685 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.693 / SU Rfree Blow DPI: 0.327 / SU Rfree Cruickshank DPI: 0.332
RfactorNum. reflection% reflectionSelection details
Rfree0.246 964 5 %RANDOM
Rwork0.192 ---
obs0.195 19275 100 %-
Displacement parametersBiso mean: 106.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.2464 Å20 Å20 Å2
2---1.2464 Å20 Å2
3---2.4929 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.92→81.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 0 0 4131
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014237HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185770HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1409SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes705HARMONIC5
X-RAY DIFFRACTIONt_it4237HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion18.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion557SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4569SEMIHARMONIC4
LS refinement shellResolution: 2.92→2.94 Å / Total num. of bins used: 48
RfactorNum. reflection% reflection
Rfree0.4041 -4.98 %
Rwork0.2531 382 -
all0.2601 402 -
obs--99.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4744-1.41151.2514.3420.00862.72980.19590.5711-0.6434-0.14630.1279-0.18590.65240.6289-0.3238-0.2450.18840.304-0.26750.18570.17255.8902-2.242920.546
22.28560.3078-1.53081.7953-2.80873.5671-0.2895-0.0687-0.7461-0.2474-0.2778-0.15770.52560.33850.5673-0.17470.07130.189-0.1950.05120.0339.574729.8032-2.7886
31.23140.0452-0.06351.4062-1.27271.9127-0.14070.0309-0.2287-0.0692-0.06810.0584-0.05640.05520.2088-0.07650.01430.0807-0.07810.0057-0.0471-0.462845.0698-3.2184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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