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- PDB-6tr7: N-[2-(5-fluoro-1H-indol-3-yl)ethyl]acetamide-Notum complex -

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Basic information

Entry
Database: PDB / ID: 6tr7
TitleN-[2-(5-fluoro-1H-indol-3-yl)ethyl]acetamide-Notum complex
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsONCOPROTEIN / Wnt receptor Frizzled8 carbamazepine
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-HWH / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsZhao, Y. / Jones, E.Y.
CitationJournal: J. Pineal Res. / Year: 2020
Title: Structural characterization of melatonin as an inhibitor of the Wnt deacylase Notum.
Authors: Zhao, Y. / Ren, J. / Hillier, J. / Jones, M. / Lu, W. / Jones, E.Y.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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)45,55022
Polymers43,5671
Non-polymers1,98321
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-36 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.307, 73.365, 79.020
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
#4: 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: isolated from a genetically manipulated source
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, 170 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-HWH / ~{N}-[2-(5-fluoranyl-1~{H}-indol-3-yl)ethyl]ethanamide


Mass: 220.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13FN2O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.01 Å3/Da / Density % sol: 38.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.5 M ammonium sulphate 0.1 M sodium citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.47→79.02 Å / Num. obs: 60282 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 1 / Net I/σ(I): 12.7
Reflection shellResolution: 1.47→1.5 Å / Num. unique obs: 2889 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UZQ

4uzq


Resolution: 1.47→53.765 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2195 3011 5.05 %
Rwork0.1962 --
obs0.1974 59603 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.92 Å2 / Biso mean: 23.8728 Å2 / Biso min: 10.63 Å2
Refinement stepCycle: final / Resolution: 1.47→53.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 124 150 3084
Biso mean--44.09 31.3 -
Num. residues----350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.47-1.4930.44411120.3814242994
1.493-1.51750.34341260.3527247697
1.5-40.2031860.1882761100
1.5175-1.54370.34451340.3169251498
1.5437-1.57170.30111160.2947253298
1.5717-1.6020.2961330.2842254998
1.602-1.63470.26531220.26254398
1.6347-1.67020.33951210.2691255498
1.6702-1.70910.30211250.2447254999
1.7091-1.75180.23941260.2368255199
1.7518-1.79920.23241230.22258399
1.7992-1.85210.22761530.2127254799
1.8521-1.91190.28231520.1989254699
1.9119-1.98020.22271440.1864258399
1.9802-2.05950.21951380.1748257399
2.0595-2.15330.19811630.1755256699
2.1533-2.26680.21631400.16822571100
2.2668-2.40880.23751290.17612619100
2.4088-2.59480.22731450.18152591100
2.5948-2.85590.19281370.17862638100
2.8559-3.26910.1871500.17932627100
3.2691-4.11850.17741360.16952690100
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)
11.00840.1299-0.08311.14630.32581.3954-0.01480.00380.16920.0048-0.00190.0022-0.19850.0230.00610.1567-0.0088-0.01670.11750.01340.16117.575910.4987-0.5057
21.04840.0861-0.08011.6879-0.36840.8056-0.0175-0.03890.0090.12560.03660.1417-0.1242-0.0537-0.02480.12530.0050.00680.13910.01210.1435-0.3645-1.7328-3.1593
32.0081.07970.71982.05281.27561.48090.0483-0.12980.14430.0762-0.11130.2899-0.0572-0.22630.07850.14710.00810.03350.18460.00330.2077-10.5318-2.06034.9737
40.5064-0.1914-0.12540.79590.04850.3792-0.0276-0.008-0.0847-0.01460.0264-0.02180.0670.03760.01090.1183-0.00740.00040.14990.00980.14117.721-12.6454-5.4972
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 452 )A321 - 452

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