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- PDB-7bn5: Notum fragment_1 (2-(isoquinolin-1-ylsulfanyl)acetic acid) -

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Basic information

Entry
Database: PDB / ID: 7bn5
TitleNotum fragment_1 (2-(isoquinolin-1-ylsulfanyl)acetic acid)
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
2-isoquinolin-1-ylsulfanylethanoic acid / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: To Be Published
Title: Notum Inhibitor
Authors: Zhao, Y. / Jones, E.Y.
History
DepositionJan 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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

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Assembly

Deposited unit
A: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3887
Polymers43,5671
Non-polymers8216
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-32 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.580, 71.270, 78.840
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: 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, 32 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-U4K / 2-isoquinolin-1-ylsulfanylethanoic acid / (Isoquinolin-1-ylsulfanyl)-acetic acid / 2-(Isoquinolin-1-ylthio)acetic acid


Mass: 219.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 35.97 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
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 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.22→59.58 Å / Num. obs: 17080 / % possible obs: 99.6 % / Redundancy: 12.1 % / CC1/2: 0.999 / Net I/σ(I): 20.7
Reflection shellResolution: 2.22→2.26 Å / Num. unique obs: 768 / CC1/2: 0.523

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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: 4uz1

4uz1


Resolution: 2.22→52.87 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 826 4.85 %
Rwork0.2127 16208 -
obs0.2147 17034 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.57 Å2 / Biso mean: 51.4891 Å2 / Biso min: 29.74 Å2
Refinement stepCycle: final / Resolution: 2.22→52.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 50 27 2834
Biso mean--66.04 45.74 -
Num. residues----347
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.360.29681330.2682537267096
2.36-2.540.321230.260127122835100
2.54-2.80.27651260.240726832809100
2.8-3.20.25351500.225527002850100
3.2-4.030.25421350.205527272862100
4.03-52.870.23621590.191628493008100
Refinement TLS params.Method: refined / Origin x: 4.8651 Å / Origin y: -1.0144 Å / Origin z: -2.6822 Å
111213212223313233
T0.3555 Å2-0.0142 Å2-0.0162 Å2-0.3756 Å20.0777 Å2--0.3533 Å2
L1.0772 °20.4137 °2-0.2551 °2-0.9393 °2-0.3562 °2--0.8409 °2
S-0.0346 Å °0.0705 Å °0.057 Å °-0.0225 Å °0.0493 Å °0.0132 Å °-0.1587 Å °-0.0657 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA87 - 1401
2X-RAY DIFFRACTION1allA1501

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