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- PDB-6y8i: Fragment KCL_I013 in complex with IL-1-beta -

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Basic information

Entry
Database: PDB / ID: 6y8i
TitleFragment KCL_I013 in complex with IL-1-beta
ComponentsInterleukin-1 beta
KeywordsSIGNALING PROTEIN / FBDD / FRAGMENT BASED DRUG DESIGN / XCHEM / IL1B
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / positive regulation of tight junction disassembly / positive regulation of prostaglandin biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of neuroinflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of monocyte chemotactic protein-1 production / positive regulation of p38MAPK cascade / negative regulation of synaptic transmission / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of vascular endothelial growth factor production / positive regulation of cell division / positive regulation of glial cell proliferation / regulation of neurogenesis / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / positive regulation of epithelial to mesenchymal transition / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / negative regulation of MAPK cascade / JNK cascade / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / neutrophil chemotaxis / embryo implantation / astrocyte activation / positive regulation of interleukin-2 production / regulation of insulin secretion / positive regulation of mitotic nuclear division / response to interleukin-1 / negative regulation of insulin receptor signaling pathway / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / Interleukin-1 signaling / negative regulation of neurogenesis / positive regulation of interleukin-6 production / integrin binding / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / positive regulation of inflammatory response / cytokine-mediated signaling pathway / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / apoptotic process / positive regulation of gene expression
Similarity search - Function
Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / 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) ...Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / 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
1-(5-bromanylpyridin-2-yl)-3-(2-hydroxyethyl)urea / Interleukin-1 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsDe Nicola, G.F. / Nichols, C.E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
British Heart FoundationSP/14/2/30922, FS/14/29/30896 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17164 United Kingdom
CitationJournal: To Be Published
Title: Fragment KCL_I013 in complex with IL-1-beta
Authors: De Nicola, G.F. / Nichols, C.E.
History
DepositionMar 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7523
Polymers17,3961
Non-polymers3562
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area7680 Å2
Unit cell
Length a, b, c (Å)54.790, 54.790, 75.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Interleukin-1 beta / IL-1 beta / Catabolin


Mass: 17395.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-OGE / 1-(5-bromanylpyridin-2-yl)-3-(2-hydroxyethyl)urea


Mass: 260.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10BrN3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.8M ammonium sulphate and 0.1M Tris pH7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.46→37.79 Å / Num. obs: 37604 / % possible obs: 97 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.27 Å2 / CC1/2: 1 / Net I/σ(I): 16.9
Reflection shellResolution: 1.46→1.49 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1878 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
GDAdata collection
PHENIX1.16_3549refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5R85

5r85


Resolution: 1.46→24.5 Å / SU ML: 0.2014 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.7472
RfactorNum. reflection% reflection
Rfree0.2627 3587 4.91 %
Rwork0.2385 --
obs0.2397 37594 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.51 Å2
Refinement stepCycle: LAST / Resolution: 1.46→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 19 22 1157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531200
X-RAY DIFFRACTIONf_angle_d0.82231629
X-RAY DIFFRACTIONf_chiral_restr0.0937182
X-RAY DIFFRACTIONf_plane_restr0.0052221
X-RAY DIFFRACTIONf_dihedral_angle_d2.9857940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.480.39771140.34922715X-RAY DIFFRACTION95.45
1.48-1.50.34821260.33232691X-RAY DIFFRACTION96.34
1.5-1.520.35011500.33622651X-RAY DIFFRACTION95.92
1.52-1.540.35361380.32642680X-RAY DIFFRACTION95.75
1.54-1.570.36121980.32442638X-RAY DIFFRACTION96.73
1.57-1.590.28341220.30242674X-RAY DIFFRACTION96.48
1.59-1.620.29331250.28692751X-RAY DIFFRACTION96.51
1.62-1.650.31711470.28072656X-RAY DIFFRACTION96.66
1.65-1.680.27461710.26392646X-RAY DIFFRACTION96.64
1.68-1.720.26121340.25622755X-RAY DIFFRACTION96.56
1.72-1.750.22811330.24652730X-RAY DIFFRACTION96.85
1.75-1.790.23781440.25172681X-RAY DIFFRACTION97.41
1.79-1.840.28821690.25062693X-RAY DIFFRACTION97.51
1.84-1.890.31211290.23942767X-RAY DIFFRACTION97.54
1.89-1.940.32581070.24492744X-RAY DIFFRACTION97.7
1.94-2.010.24071590.25362661X-RAY DIFFRACTION97.75
2.01-2.080.28731110.2452789X-RAY DIFFRACTION98.11
2.08-2.160.27161650.23652713X-RAY DIFFRACTION97.43
2.16-2.260.26661300.24032745X-RAY DIFFRACTION98.49
2.26-2.380.3181600.24142708X-RAY DIFFRACTION97.82
2.38-2.530.29751500.24792709X-RAY DIFFRACTION97.68
2.53-2.720.26341330.25042766X-RAY DIFFRACTION98.81
2.72-30.29771100.24832808X-RAY DIFFRACTION98.92
3-3.430.22621440.23052753X-RAY DIFFRACTION98.6
3.43-4.320.21821430.20572547X-RAY DIFFRACTION91.81
4.32-24.50.2849750.23661806X-RAY DIFFRACTION64.09

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