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- PDB-7b2z: Notum complex with ARUK3003907 -

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Basic information

Entry
Database: PDB / ID: 7b2z
TitleNotum complex with ARUK3003907
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Inhibitor
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
Chem-SQW / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 28, 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

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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)44,61911
Polymers43,5671
Non-polymers1,05210
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-45 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.661, 72.165, 77.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SQW / propan-2-yl 4-indol-1-yl-4-oxidanylidene-butanoate


Mass: 259.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.11 %
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: 1.24→52.95 Å / Num. obs: 95918 / % possible obs: 100 % / Redundancy: 25.9 % / CC1/2: 1 / Net I/σ(I): 19.6
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 4739 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ARG

7arg


Resolution: 1.24→45.98 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2087 4649 4.85 %
Rwork0.1958 91148 -
obs0.1965 95797 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.54 Å2 / Biso mean: 23.1365 Å2 / Biso min: 12.06 Å2
Refinement stepCycle: final / Resolution: 1.24→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 56 108 2936
Biso mean--34.97 26.34 -
Num. residues----345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.24-1.250.30661450.299530203165
1.25-1.270.29841400.281430113151
1.27-1.280.29731470.269530233170
1.28-1.30.25141300.261130193149
1.3-1.320.28381630.249429673130
1.32-1.340.28251540.245130053159
1.34-1.350.27931510.226930403191
1.35-1.380.2391480.223529623110
1.38-1.40.21011480.213430513199
1.4-1.420.23891620.211230093171
1.42-1.440.23271740.202729793153
1.44-1.470.20851590.19730023161
1.47-1.50.23051610.190330063167
1.5-1.530.20411640.18730053169
1.53-1.560.18731470.175930613208
1.56-1.60.19371460.177529973143
1.6-1.640.1881480.178730333181
1.64-1.680.17841490.177730343183
1.68-1.730.19051420.17730413183
1.73-1.790.17151490.172530263175
1.79-1.850.21021510.180330613212
1.85-1.930.19871690.181230083177
1.93-2.010.20091550.181130353190
2.01-2.120.20841550.185330763231
2.12-2.250.18711600.181530553215
2.25-2.430.23251700.195730473217
2.43-2.670.20751690.203730833252
2.67-3.060.21411520.207130943246
3.06-3.850.19561690.200631113280
3.85-45.980.20991720.190832873459
Refinement TLS params.Method: refined / Origin x: 25.2988 Å / Origin y: 70.8183 Å / Origin z: 80.6998 Å
111213212223313233
T0.1381 Å2-0.0013 Å2-0.0001 Å2-0.124 Å2-0.0161 Å2--0.1418 Å2
L0.6318 °2-0.0585 °20.0495 °2-0.9726 °20.077 °2--0.6939 °2
S-0.0209 Å °0.0173 Å °0.0136 Å °-0.0328 Å °0.0148 Å °-0.0103 Å °-0.0831 Å °0.0253 Å °0.0051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 1901
2X-RAY DIFFRACTION1allS2 - 243
3X-RAY DIFFRACTION1allB1 - 4

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