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- PDB-7b3f: Notum S232A in complex with ARUK3003718 -

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Basic information

Entry
Database: PDB / ID: 7b3f
TitleNotum S232A in complex with ARUK3003718
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / 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-SRK / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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 30, 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 1.3Nov 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)44,73412
Polymers43,5511
Non-polymers1,18311
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-32 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.305, 71.256, 78.296
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: 43551.148 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, 99 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 78.133 Da / Num. of mol.: 3 / 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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SRK / 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid


Mass: 219.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 36.31 %
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: 1.39→47.78 Å / Num. obs: 68561 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 11.7
Reflection shellResolution: 1.39→1.41 Å / Num. unique obs: 3349 / CC1/2: 0.462

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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: 7AGR

7agr


Resolution: 1.39→47.78 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 3400 4.97 %
Rwork0.1897 64966 -
obs0.191 68366 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.66 Å2 / Biso mean: 24.7805 Å2 / Biso min: 12.8 Å2
Refinement stepCycle: final / Resolution: 1.39→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 70 89 2992
Biso mean--35.79 27.97 -
Num. residues----355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.39-1.410.36141370.36562599273697
1.41-1.430.35771500.32922666281699
1.43-1.450.31331590.304126352794100
1.45-1.480.28811370.279726702807100
1.48-1.50.27551350.255526752810100
1.5-1.530.28091320.250926942826100
1.53-1.560.26661290.229826892818100
1.56-1.590.24281460.228426772823100
1.59-1.630.2481470.216727002847100
1.63-1.660.27571240.207426762800100
1.66-1.710.23011500.197326952845100
1.71-1.750.24721380.185726782816100
1.75-1.80.21581400.172326972837100
1.8-1.860.20781240.169327152839100
1.86-1.930.21091440.170627012845100
1.93-20.18971710.171826862857100
2-2.10.18541510.163827082859100
2.1-2.210.17261450.16326982843100
2.21-2.340.2281450.172227252870100
2.34-2.530.19111390.179627462885100
2.53-2.780.24451320.188527302862100
2.78-3.180.21311450.190927752920100
3.18-4.010.21711350.180527982933100
4.01-47.780.19091450.186429333078100
Refinement TLS params.Method: refined / Origin x: 25.7169 Å / Origin y: 69.9285 Å / Origin z: 80.2548 Å
111213212223313233
T0.1231 Å2-0.0061 Å2-0.0064 Å2-0.1225 Å2-0.0148 Å2--0.1212 Å2
L0.8193 °2-0.077 °2-0.162 °2-1.0918 °2-0.0549 °2--0.7179 °2
S-0.0039 Å °-0.0216 Å °0.0088 Å °-0.0223 Å °0.0029 Å °0.0051 Å °-0.0257 Å °0.0282 Å °0.004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA87 - 510
2X-RAY DIFFRACTION1allA601 - 689
3X-RAY DIFFRACTION1allA511

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