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- PDB-6p9e: Crystal structure of IL-36gamma complexed to A-552 -

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Basic information

Entry
Database: PDB / ID: 6p9e
TitleCrystal structure of IL-36gamma complexed to A-552
ComponentsInterleukin-36 gamma
KeywordsCYTOKINE / IL-36 / small molecule antagonist
Function / homology
Function and homology information


Interleukin-36 pathway / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / cytokine activity / cytokine-mediated signaling pathway / cell-cell signaling / cellular response to lipopolysaccharide / innate immune response / positive regulation of gene expression / extracellular space ...Interleukin-36 pathway / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / cytokine activity / cytokine-mediated signaling pathway / cell-cell signaling / cellular response to lipopolysaccharide / innate immune response / positive regulation of gene expression / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Chem-O6D / Interleukin-36 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArgiriadi, M.A. / Todorovic, T. / Su, Z. / Putman, B. / Kakavas, S.J. / Salte, K.M. / McDonald, H.A. / Wetter, J.B. / Paulsboe, S.E. / Sun, Q. ...Argiriadi, M.A. / Todorovic, T. / Su, Z. / Putman, B. / Kakavas, S.J. / Salte, K.M. / McDonald, H.A. / Wetter, J.B. / Paulsboe, S.E. / Sun, Q. / Gerstein, C.E. / Medina, L. / Sielaff, B. / Sadhukhan, R. / Stockmann, H. / Richardson, P.L. / Qiu, W. / Henry, R.F. / Herold, J.M. / Shotwell, J.B. / McGaraughty, S.P. / Honore, P. / Gopalakrishnan, S.M. / Sun, C.C. / Scott, V.E.
CitationJournal: Sci Rep / Year: 2019
Title: Small Molecule IL-36 gamma Antagonist as a Novel Therapeutic Approach for Plaque Psoriasis.
Authors: Todorovic, V. / Su, Z. / Putman, C.B. / Kakavas, S.J. / Salte, K.M. / McDonald, H.A. / Wetter, J.B. / Paulsboe, S.E. / Sun, Q. / Gerstein, C.E. / Medina, L. / Sielaff, B. / Sadhukhan, R. / ...Authors: Todorovic, V. / Su, Z. / Putman, C.B. / Kakavas, S.J. / Salte, K.M. / McDonald, H.A. / Wetter, J.B. / Paulsboe, S.E. / Sun, Q. / Gerstein, C.E. / Medina, L. / Sielaff, B. / Sadhukhan, R. / Stockmann, H. / Richardson, P.L. / Qiu, W. / Argiriadi, M.A. / Henry, R.F. / Herold, J.M. / Shotwell, J.B. / McGaraughty, S.P. / Honore, P. / Gopalakrishnan, S.M. / Sun, C.C. / Scott, V.E.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-36 gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5152
Polymers17,0451
Non-polymers4701
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.420, 96.420, 96.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Interleukin-36 gamma / IL-1-related protein 2 / IL-1RP2 / Interleukin-1 epsilon / IL-1 epsilon / Interleukin-1 family ...IL-1-related protein 2 / IL-1RP2 / Interleukin-1 epsilon / IL-1 epsilon / Interleukin-1 family member 9 / IL-1F9 / Interleukin-1 homolog 1 / IL-1H1


Mass: 17045.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL36G, IL1E, IL1F9, IL1H1, IL1RP2, UNQ2456/PRO5737 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZH8
#2: Chemical ChemComp-O6D / (2S)-2-{[4-(3-amino-4-methylphenyl)-6-methylpyrimidin-2-yl]oxy}-3-methoxy-3,3-diphenylpropanoic acid


Mass: 469.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 3 M NaCl, 0.1 M Na3 Citrate, pH 3.5

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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 PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.4 Å / Num. obs: 9984 / % possible obs: 100 % / Redundancy: 18.4 % / Biso Wilson estimate: 39.41 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 28.8
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.57 / Num. unique obs: 533

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IZE

4ize


Resolution: 2→30.49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.242 497 4.98 %RANDOM
Rwork0.216 ---
obs0.217 9982 97.5 %-
Displacement parametersBiso mean: 44.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2→30.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 35 53 1224
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011205HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.171651HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d392SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes229HARMONIC5
X-RAY DIFFRACTIONt_it1205HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion19.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion163SEMIHARMONIC5
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_contact1381SEMIHARMONIC4
LS refinement shellResolution: 2→2.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3371 129 4.84 %
Rwork0.2429 2537 -
all0.2473 2666 -
obs--93.17 %

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