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- PDB-6zuv: Notum fragment 286 -

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Basic information

Entry
Database: PDB / ID: 6zuv
TitleNotum fragment 286
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsSIGNALING PROTEIN / Wnt Notum inhibitor complex
Function / homology
Function and homology information


[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / negative regulation of canonical Wnt signaling pathway / bone development ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / Release of Hh-Np from the secreting cell / phospholipase C activity / 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
[1-(4-chlorophenyl)-1,2,3-triazol-4-yl]methanol / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M000141/1 United Kingdom
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: 5-Phenyl-1,3,4-oxadiazol-2(3 H )-ones Are Potent Inhibitors of Notum Carboxylesterase Activity Identified by the Optimization of a Crystallographic Fragment Screening Hit.
Authors: Mahy, W. / Willis, N.J. / Zhao, Y. / Woodward, H.L. / Svensson, F. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Hillier, J. / Kjaer, S. / Frew, S. / Monaghan, A. / Bictash, M. / Salinas, P.C. ...Authors: Mahy, W. / Willis, N.J. / Zhao, Y. / Woodward, H.L. / Svensson, F. / Sipthorp, J. / Vecchia, L. / Ruza, R.R. / Hillier, J. / Kjaer, S. / Frew, S. / Monaghan, A. / Bictash, M. / Salinas, P.C. / Whiting, P. / Vincent, J.P. / Jones, E.Y. / Fish, P.V.
History
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)44,76112
Polymers43,5671
Non-polymers1,19311
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-66 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.673, 72.284, 79.001
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 / N-Acetylglucosamine


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 , 4 types, 143 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-B1J / [1-(4-chlorophenyl)-1,2,3-triazol-4-yl]methanol


Mass: 209.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8ClN3O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.2
Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.54→79.1 Å / Num. obs: 52038 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.99 / Net I/σ(I): 10
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 2476 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TR5

6tr5


Resolution: 1.54→53.33 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2522 4.9 %
Rwork0.2099 48949 -
obs0.2122 51471 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.33 Å2 / Biso mean: 27.5284 Å2 / Biso min: 11.26 Å2
Refinement stepCycle: final / Resolution: 1.54→53.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 76 133 3050
Biso mean--42.77 31.92 -
Num. residues----355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.54-1.570.40091310.36852555268694
1.57-1.60.39581200.36222649276997
1.6-1.640.3851360.3412626276297
1.64-1.680.37051260.32172655278198
1.68-1.720.31981410.30282689283099
1.72-1.760.34151530.29752665281899
1.76-1.820.30671470.265527082855100
1.82-1.870.27731350.25032701283699
1.87-1.940.3091520.22322691284399
1.94-2.020.24331360.21192739287599
2.02-2.110.26171330.201127122845100
2.11-2.220.24581360.187327472883100
2.22-2.360.23831680.194227152883100
2.36-2.540.22061310.196727672898100
2.54-2.80.25661300.197227792909100
2.8-3.20.24681480.196327822930100
3.2-4.040.23881380.180628282966100
4.04-53.330.23621610.188829413102100
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)
11.04050.11-0.53021.29160.41612.3049-0.0090.0360.13670.0440.00030.0022-0.21510.0156-0.00030.1764-0.0018-0.01940.12420.01750.17697.438410.4868-0.4075
21.6012-0.2417-0.08272.1258-0.13350.2526-0.0489-0.02280.02010.17550.01850.1125-0.1303-0.0903-0.01040.12960.00130.01280.13590.00080.1292-0.6587-2.0457-1.6275
34.66262.25341.38725.56182.53362.92660.1374-0.23030.26650.0869-0.2490.3229-0.1248-0.19530.0530.1345-0.0070.03790.16680.00360.1867-10.7338-2.07434.7566
40.9139-0.1037-0.48261.5686-0.89491.7706-0.0644-0.0134-0.119-0.0766-0.0285-0.13290.1250.12480.10130.1484-0.00270.01290.1606-0.00620.19378.379-14.3361-5.6032
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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