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- PDB-6tr5: Melatonin-Notum complex -

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Basic information

Entry
Database: PDB / ID: 6tr5
TitleMelatonin-Notum complex
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Wnt Notum inhibitor melatonin
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
N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.509 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. 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 15, 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_id_ISSN ..._chem_comp.type / _citation.journal_id_ISSN / _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

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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)45,10013
Polymers43,5671
Non-polymers1,53212
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-79 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.259, 73.165, 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
#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, 127 molecules

#2: Chemical ChemComp-ML1 / N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide / Melatonin


Mass: 232.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2 Å3/Da / Density % sol: 38.46 %
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: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.509→73.17 Å / Num. obs: 55371 / % possible obs: 99.6 % / Redundancy: 11 % / CC1/2: 1 / Net I/σ(I): 15
Reflection shellResolution: 1.51→1.54 Å / Num. unique obs: 2562 / CC1/2: 0.54

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Processing

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

4uzq


Resolution: 1.509→53.68 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2808 5.13 %
Rwork0.1964 51977 -
obs0.1979 54785 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90 Å2 / Biso mean: 27.4968 Å2 / Biso min: 13 Å2
Refinement stepCycle: final / Resolution: 1.509→53.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 92 117 2966
Biso mean--56.18 33.36 -
Num. residues----345
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5093-1.53530.40831460.3765233291
1.5353-1.56320.38221320.3517247095
1.5632-1.59330.38761380.3323248195
1.5933-1.62580.32591240.3109257097
1.6258-1.66120.34031350.293256798
1.6612-1.69980.27061520.262253899
1.6998-1.74230.30281410.2464259499
1.7423-1.78940.27121190.2186260599
1.7894-1.84210.23411400.2133258899
1.8421-1.90150.22521250.1983262099
1.9015-1.96950.22781350.18512614100
1.9695-2.04840.22211320.18142623100
2.0484-2.14160.22271560.18422602100
2.1416-2.25450.20471480.17762633100
2.2545-2.39570.2381540.1822608100
2.3957-2.58070.18851440.18852638100
2.5807-2.84040.23781630.19052650100
2.8404-3.25140.22211560.18412662100
3.2514-4.09620.18931590.17152702100
4.0962-53.680.19871090.18482880100
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)
10.6497-0.1078-0.31241.036-0.34850.7068-0.04590.0328-0.0992-0.0628-0.0006-0.07850.05890.0469-0.00010.1176-0.01910.00430.15540.01060.1498.3626-14.6874-5.7761
22222222.37860.24010.68234.5398-3.11095.4692-0.1511-4.29710.7260.8397-0.17070.09280.858-0.28010.70324.2095-10.85712.2161
31.05590.13010.24961.37980.54640.37520.03240.02630.20430.0271-0.04150.0102-0.293-0.00960.00050.1989-0.0075-0.00920.1450.00850.19047.813110.88911.2456
41.01880.1661-0.01250.91850.170.9616-0.0260.05210.21890.02650.03660.0172-0.1794-0.0198-0.00020.1784-0.0031-0.0120.13190.03580.1765.62938.8049-3.7583
51.1560.253-0.0980.80290.30490.2687-0.0239-0.04560.09990.0603-0.06090.1635-0.0542-0.0273-0.00540.15380.0071-0.00140.19040.01390.1813-5.6767-4.09042.0125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 321 through 451 )A321 - 451
2X-RAY DIFFRACTION2chain 'A' and (resid 452 through 452 )A452
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 142 )A87 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 252 )A143 - 252
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 320 )A253 - 320

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