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- PDB-5r8j: PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z... -

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Basic information

Entry
Database: PDB / ID: 5r8j
TitlePanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z355728146 in complex with INTERLEUKIN-1 BETA
ComponentsInterleukin-1 beta
KeywordsSIGNALING PROTEIN / IL-1 BETA / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production ...smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / sequestering of triglyceride / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / positive regulation of neuroinflammatory response / response to carbohydrate / regulation of defense response to virus by host / interleukin-1 receptor binding / positive regulation of fever generation / fever generation / Interleukin-1 processing / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of canonical NF-kappaB signal transduction / negative regulation of synaptic transmission / positive regulation of membrane protein ectodomain proteolysis / positive regulation of granulocyte macrophage colony-stimulating factor production / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / response to ATP / Interleukin-10 signaling / positive regulation of cell division / ectopic germ cell programmed cell death / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Pyroptosis / positive regulation of vascular endothelial growth factor production / negative regulation of lipid catabolic process / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of T cell proliferation / negative regulation of MAP kinase activity / positive regulation of glial cell proliferation / JNK cascade / negative regulation of insulin receptor signaling pathway / neutrophil chemotaxis / positive regulation of interleukin-2 production / embryo implantation / regulation of insulin secretion / regulation of ERK1 and ERK2 cascade / response to interleukin-1 / positive regulation of mitotic nuclear division / positive regulation of protein export from nucleus / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of DNA-binding transcription factor activity / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / negative regulation of neurogenesis / cellular response to mechanical stimulus / positive regulation of inflammatory response / Interleukin-1 signaling / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / immune response / positive regulation of protein phosphorylation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / 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
Chem-S8D / Interleukin-1 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.62 Å
AuthorsDe Nicola, G.F. / Nichols, C.E.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 ...Title: Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.
Authors: Nichols, C. / Ng, J. / Keshu, A. / Kelly, G. / Conte, M.R. / Marber, M.S. / Fraternali, F. / De Nicola, G.F.
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7884
Polymers17,3961
Non-polymers3923
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.600, 54.600, 75.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-S8D / 2-[(2~{R},5~{S})-2,5-dimethylmorpholin-4-yl]-~{N}-ethyl-ethanamide


Mass: 200.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.23 Å3/Da / Density % sol: 61.87 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 2.8M ammonium sulphate, 0.1M Tris pH7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96871 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96871 Å / Relative weight: 1
ReflectionResolution: 1.62→44.2 Å / Num. obs: 28133 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 13.1 / Num. measured all: 186698 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.62-1.666.61.8711386620960.3990.7852.0311.1100
7.24-44.25.90.04519733360.9970.020.0538.199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2NVH

2nvh


Resolution: 1.62→44.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.762 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 1386 4.9 %RANDOM
Rwork0.1893 ---
obs0.1905 26713 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.64 Å2 / Biso mean: 29.932 Å2 / Biso min: 15.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 1.62→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 24 92 1306
Biso mean--58.53 36.87 -
Num. residues----152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0152833
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171976
X-RAY DIFFRACTIONr_angle_refined_deg1.631.6592925
X-RAY DIFFRACTIONr_angle_other_deg1.3431.6134648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8735304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13824.82887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24915392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.624156
X-RAY DIFFRACTIONr_chiral_restr0.080.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022569
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02421
X-RAY DIFFRACTIONr_mcbond_it2.3113.0921534
X-RAY DIFFRACTIONr_mcbond_other2.3273.0661513
X-RAY DIFFRACTIONr_mcangle_it4.124.3661454
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 100 -
Rwork0.331 1987 -
all-2087 -
obs--100 %

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