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- PDB-7arg: Notum in complex with ARUK3002704 -

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Basic information

Entry
Database: PDB / ID: 7arg
TitleNotum in complex with ARUK3002704
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsSIGNALING PROTEIN / Notum inhibitor
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-RW8 / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/M000141/1 United Kingdom
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
DepositionOct 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Data collection / Database references
Category: citation / database_2 / diffrn_radiation_wavelength
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 / _diffrn_radiation_wavelength.wavelength
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)44,98615
Polymers43,5671
Non-polymers1,41914
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-39 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.730, 71.780, 78.020
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 , 5 types, 143 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-RW8 / methyl 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoate


Mass: 233.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 35.92 %
Crystal growTemperature: 296 K / Method: evaporation / Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citric, pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.24→59.7 Å / Num. obs: 95627 / % possible obs: 100 % / Redundancy: 39.4 % / CC1/2: 1 / Net I/σ(I): 16.8
Reflection shellResolution: 1.24→1.26 Å / Rmerge(I) obs: 1.5 / Num. unique obs: 4756 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TV4

6tv4


Resolution: 1.24→52.82 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 4759 4.99 %
Rwork0.1803 90556 -
obs0.1812 95315 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.83 Å2 / Biso mean: 28.0147 Å2 / Biso min: 14.43 Å2
Refinement stepCycle: final / Resolution: 1.24→52.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 89 130 3070
Biso mean--45.6 34.85 -
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 (%)
1.24-1.250.30741420.27962987312999
1.25-1.270.27431760.26122931310799
1.27-1.280.25411570.249729713128100
1.28-1.30.25351700.23812979314999
1.3-1.320.26451540.23672963311799
1.32-1.340.24881820.222329533135100
1.34-1.350.2351450.22173012315799
1.35-1.380.2421690.219729593128100
1.38-1.40.25321550.218729983153100
1.4-1.420.25511700.21329653135100
1.42-1.440.19811660.193129793145100
1.44-1.470.22671610.191529923153100
1.47-1.50.22231770.182429683145100
1.5-1.530.19381700.182529953165100
1.53-1.560.1841350.17130203155100
1.56-1.60.17621420.175429983140100
1.6-1.640.23241530.171330273180100
1.64-1.680.1811830.173629733156100
1.68-1.730.20181670.173730193186100
1.73-1.790.20011560.166530393195100
1.79-1.850.19261590.169930103169100
1.85-1.930.1931550.173130443199100
1.93-2.010.19261690.169229903159100
2.01-2.120.17781680.173130573225100
2.12-2.250.18361410.169930553196100
2.25-2.430.19351320.178930703202100
2.43-2.670.21111530.18830923245100
2.67-3.060.20321570.183430893246100
3.06-3.850.18831610.174731133274100
3.85-52.820.19071340.177233083442100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.98370.1313-0.05331.1993-0.11562.0303-0.02440.0157-0.11950.04370.02330.01290.2470.0239-0.02090.20090.0010.01140.1459-0.01720.1972-7.4437-10.2862-0.5936
21.44780.13750.25983.32411.58591.5894-0.0124-0.05-0.01560.27130.0043-0.11550.22290.0697-0.05980.1432-0.0004-0.01130.1430.00770.13580.26811.9562-1.973
34.14592.5589-0.44645.2242-2.75822.65730.1769-0.6292-0.20270.1552-0.3754-0.3560.00330.20780.16760.1464-0.0116-0.04130.270.00550.190110.59141.94624.5829
40.9022-0.14970.32561.10970.47140.9339-0.0279-0.03170.0955-0.05670.00550.0867-0.0791-0.05130.03750.1517-0.0054-0.00230.15710.00740.1722-7.858714.1835-6.246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 88 through 224 )A88 - 224
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 286 )A225 - 286
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 320 )A287 - 320
4X-RAY DIFFRACTION4chain 'A' and (resid 321 through 451 )A321 - 451

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