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- PDB-7b4x: Notum complex with ARUK3002697 -

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Basic information

Entry
Database: PDB / ID: 7b4x
TitleNotum complex with ARUK3002697
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Inhibitor complex
Function / homology
Function and homology information


protein-containing complex destabilizing activity / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway ...protein-containing complex destabilizing activity / [Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular region
Similarity search - Function
Pectinacetylesterase/NOTUM / Pectinacetylesterase
Similarity search - Domain/homology
Chem-SWT / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsJones, E.Y. / Fish, P.
CitationJournal: Acs Chem Neurosci / Year: 2022
Title: Structural Analysis and Development of Notum Fragment Screening Hits.
Authors: Zhao, Y. / Mahy, W. / Willis, N.J. / Woodward, H.L. / Steadman, D. / Bayle, E.D. / Atkinson, B.N. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Harlos, K. / Jeganathan, F. / Constantinou, S. / ...Authors: Zhao, Y. / Mahy, W. / Willis, N.J. / Woodward, H.L. / Steadman, D. / Bayle, E.D. / Atkinson, B.N. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Harlos, K. / Jeganathan, F. / Constantinou, S. / Costa, A. / Kjaer, S. / Bictash, M. / Salinas, P.C. / Whiting, P. / Vincent, J.P. / Fish, P.V. / Jones, E.Y.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,98116
Polymers43,5671
Non-polymers1,41315
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-56 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.193, 72.995, 77.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Palmitoleoyl-protein carboxylesterase NOTUM / hNOTUM


Mass: 43567.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Production host: Homo sapiens (human)
References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase

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Non-polymers , 5 types, 143 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SWT / 6-(4-methylphenyl)sulfanyl-2~{H}-[1,2,4]triazolo[4,3-b]pyridazin-3-one


Mass: 258.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N4OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 296 K / Method: evaporation / pH: 4.2 / Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.24→77.7 Å / Num. obs: 95744 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 10.2
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 4548 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ARG

7arg


Resolution: 1.24→53.21 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 4576 4.87 %
Rwork0.2024 89353 -
obs0.2032 93929 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.9 Å2 / Biso mean: 24.5443 Å2 / Biso min: 13.17 Å2
Refinement stepCycle: final / Resolution: 1.24→53.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 81 128 2912
Biso mean--39.03 30.17 -
Num. residues----343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.24-1.250.40621040.37012165226971
1.25-1.270.36481290.36672631276088
1.27-1.280.3331430.36552722286590
1.28-1.30.34661350.35432886302196
1.3-1.320.34391280.35742942307097
1.32-1.340.32231620.32932953311599
1.34-1.360.32661500.32752984313499
1.36-1.380.28771460.30230013147100
1.38-1.40.30581440.303630063150100
1.4-1.420.30741550.294730323187100
1.42-1.440.29051710.28130033174100
1.44-1.470.26811740.258929623136100
1.47-1.50.22941570.240230273184100
1.5-1.530.28081550.219330123167100
1.53-1.560.23451650.211630203185100
1.56-1.60.19691530.201330203173100
1.6-1.640.2121490.200330203169100
1.64-1.680.20771510.193930243175100
1.68-1.730.2271440.194930403184100
1.73-1.790.22651400.191830533193100
1.79-1.850.18281560.20230423198100
1.85-1.930.23291670.197630083175100
1.93-2.010.20661520.188930553207100
2.01-2.120.2371620.189930473209100
2.12-2.250.20221640.185330523216100
2.25-2.430.20111620.193630673229100
2.43-2.670.19421640.196230813245100
2.67-3.060.20791620.195230933255100
3.06-3.850.19281630.18231283291100
3.85-53.210.21771690.180232773446100
Refinement TLS params.Method: refined / Origin x: -4.776 Å / Origin y: 1.5689 Å / Origin z: -3.0428 Å
111213212223313233
T0.1307 Å2-0.0056 Å20.0065 Å2-0.1391 Å2-0.011 Å2--0.1327 Å2
L0.6826 °20.0442 °20.1421 °2-1.0304 °20.0926 °2--0.716 °2
S-0.0181 Å °-0.01 Å °-0.0309 Å °0.0268 Å °0.0097 Å °-0.0052 Å °0.0839 Å °-0.0084 Å °0.0095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 513
2X-RAY DIFFRACTION1allA601 - 728
3X-RAY DIFFRACTION1allA514 - 515

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