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- PDB-7b2v: Notum complex with ARUK3003906 -

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Basic information

Entry
Database: PDB / ID: 7b2v
TitleNotum complex with ARUK3003906
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Inhibitor
Function / homology
Function and homology information


[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 / bone development / negative regulation of canonical Wnt signaling pathway ...[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 / bone development / negative regulation of canonical Wnt signaling pathway / 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-SRH / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsZhao, Y. / Jone, E.Y.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structural Insights into Notum Covalent Inhibition.
Authors: Zhao, Y. / Svensson, F. / Steadman, D. / Frew, S. / Monaghan, A. / Bictash, M. / Moreira, T. / Chalk, R. / Lu, W. / Fish, P.V. / Jones, E.Y.
History
DepositionNov 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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)45,03115
Polymers43,5671
Non-polymers1,46314
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-60 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.090, 71.530, 78.010
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 / Sugars , 2 types, 2 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
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 141 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SRH / ethyl 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoate


Mass: 247.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: 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: 1.92 Å3/Da / Density % sol: 36.07 %
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 EIGER X 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→52.72 Å / Num. obs: 95831 / % possible obs: 100 % / Redundancy: 39.6 % / CC1/2: 1 / Net I/σ(I): 16.4
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 4726 / CC1/2: 0.501

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Processing

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

7arg


Resolution: 1.24→46.01 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 4771 5 %
Rwork0.1844 90737 -
obs0.1851 95508 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.18 Å2 / Biso mean: 22.9295 Å2 / Biso min: 12.4 Å2
Refinement stepCycle: final / Resolution: 1.24→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 85 128 3063
Biso mean--34.2 28.71 -
Num. residues----356
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 (%)
1.24-1.250.32721330.34872867300095
1.25-1.270.33771640.32852954311899
1.27-1.280.35771630.31232977314099
1.28-1.30.28391680.277430063174100
1.3-1.320.31971640.28582955311999
1.32-1.340.28761820.265229853167100
1.34-1.350.27811560.251929803136100
1.35-1.380.28441640.2630113175100
1.38-1.40.27311550.24130023157100
1.4-1.420.261740.232229663140100
1.42-1.440.23231600.220929963156100
1.44-1.470.2311650.209730273192100
1.47-1.50.20171820.198329663148100
1.5-1.530.22821570.188830203177100
1.53-1.560.19161410.174830183159100
1.56-1.60.14991500.170430283178100
1.6-1.640.19471520.1630223174100
1.64-1.680.19871760.162429973173100
1.68-1.730.17641690.161130303199100
1.73-1.790.18431610.156730223183100
1.79-1.850.16931610.15530113172100
1.85-1.930.18271530.160330513204100
1.93-2.010.17691700.159930203190100
2.01-2.120.17311680.159630473215100
2.12-2.250.16381420.159230783220100
2.25-2.430.19661370.177330783215100
2.43-2.670.19261480.182430983246100
2.67-3.060.2141590.183230853244100
3.06-3.850.19431640.181531233287100
3.85-46.010.19261330.190433173450100
Refinement TLS params.Method: refined / Origin x: 25.5785 Å / Origin y: 70.1383 Å / Origin z: 80.059 Å
111213212223313233
T0.1259 Å2-0.0058 Å2-0.0019 Å2-0.1347 Å2-0.0123 Å2--0.1286 Å2
L0.5746 °2-0.0516 °2-0.1159 °2-0.7324 °2-0.039 °2--0.5294 °2
S-0.0105 Å °-0.0102 Å °0.0176 Å °-0.0193 Å °-0.0007 Å °0.0061 Å °-0.029 Å °0.005 Å °0.0082 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA87 - 2201
2X-RAY DIFFRACTION1allS2 - 233
3X-RAY DIFFRACTION1allB1 - 4

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