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- PDB-8dyh: IL17A homodimer bound to Compound 6 -

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Basic information

Entry
Database: PDB / ID: 8dyh
TitleIL17A homodimer bound to Compound 6
ComponentsInterleukin-17A
KeywordsCYTOKINE / dimer / fragment / inhibitor / antagonist
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / 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 / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / immune response / protein heterodimerization activity / external side of plasma membrane / innate immune response / 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
Chem-U5X / Interleukin-17A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsArgiriadi, M.A. / Goedken, E.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2022
Title: Identification and structure-based drug design of cell-active inhibitors of interleukin 17A at a novel C-terminal site.
Authors: Goedken, E.R. / Argiriadi, M.A. / Dietrich, J.D. / Petros, A.M. / Krishnan, N. / Panchal, S.C. / Qiu, W. / Wu, H. / Zhu, H. / Adams, A.M. / Bodelle, P.M. / Goguen, L. / Richardson, P.L. / ...Authors: Goedken, E.R. / Argiriadi, M.A. / Dietrich, J.D. / Petros, A.M. / Krishnan, N. / Panchal, S.C. / Qiu, W. / Wu, H. / Zhu, H. / Adams, A.M. / Bodelle, P.M. / Goguen, L. / Richardson, P.L. / Slivka, P.F. / Srikumaran, M. / Upadhyay, A.K. / Wu, B. / Judge, R.A. / Vasudevan, A. / Gopalakrishnan, S.M. / Cox, P.B. / Stoll, V.S. / Sun, C.
History
DepositionAug 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-17A
B: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8585
Polymers29,0752
Non-polymers7843
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-28 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.516, 35.710, 45.715
Angle α, β, γ (deg.)90.000, 97.790, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 14537.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16552
#2: Chemical ChemComp-U5X / (5P)-N-benzyl-6-chloro-5-(quinolin-5-yl)pyridin-3-amine


Mass: 345.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16ClN3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion / Details: 3.2M NaCl, 0.1M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.3 Å / Num. obs: 19678 / % possible obs: 82.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 25.23 Å2 / CC1/2: 0.99 / Rsym value: 0.12 / Net I/σ(I): 6.8
Reflection shellResolution: 1.935→1.942 Å / Num. unique obs: 148 / CC1/2: 0.62 / Rsym value: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR9

4hr9


Resolution: 1.94→37.84 Å / SU ML: 0.2382 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2476 962 4.89 %
Rwork0.2116 18704 -
obs0.2134 19666 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.94 Å2
Refinement stepCycle: LAST / Resolution: 1.94→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 56 119 1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831559
X-RAY DIFFRACTIONf_angle_d1.08242129
X-RAY DIFFRACTIONf_chiral_restr0.0641234
X-RAY DIFFRACTIONf_plane_restr0.0063292
X-RAY DIFFRACTIONf_dihedral_angle_d5.0356208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.040.32411260.30142450X-RAY DIFFRACTION89.6
2.04-2.160.33291250.28892778X-RAY DIFFRACTION97.88
2.16-2.330.31571220.26372321X-RAY DIFFRACTION83.38
2.33-2.570.24631390.21432804X-RAY DIFFRACTION99.43
2.57-2.940.24741420.21082786X-RAY DIFFRACTION99.56
2.94-3.70.22231670.18222742X-RAY DIFFRACTION97.91
3.7-37.840.2221410.18822823X-RAY DIFFRACTION96.27

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