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Yorodumi- PDB-7bnc: Notum fragment_126 (2-(1,2-dihydroacenaphthylen-5-ylsulfanyl)acet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bnc | ||||||
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Title | Notum fragment_126 (2-(1,2-dihydroacenaphthylen-5-ylsulfanyl)acetic acid) | ||||||
Components | Palmitoleoyl-protein carboxylesterase NOTUM | ||||||
Keywords | HYDROLASE / 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 / bone development / Post-translational protein phosphorylation / 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 / bone development / Post-translational protein phosphorylation / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Zhao, Y. / Jones, E.Y. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Notum Inhibitor Authors: Zhao, Y. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bnc.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bnc.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 7bnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bnc_validation.pdf.gz | 763.3 KB | Display | wwPDB validaton report |
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Full document | 7bnc_full_validation.pdf.gz | 765.1 KB | Display | |
Data in XML | 7bnc_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 7bnc_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/7bnc ftp://data.pdbj.org/pub/pdb/validation_reports/bn/7bnc | HTTPS FTP |
-Related structure data
Related structure data | 7bltC 7bluC 7blwC 7bm1C 7bm3C 7bm7C 7bn5C 7bn8C 7bnbC 7bneC 7bnfC 7bnjC 7bo2C 7bo5C 4uz1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | 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 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 55 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-U5B / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.04 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→59.65 Å / Num. obs: 28943 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.86→1.89 Å / Num. unique obs: 1366 / CC1/2: 0.539 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4uz1 Resolution: 1.86→52.88 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 109.46 Å2 / Biso mean: 36.68 Å2 / Biso min: 18.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.86→52.88 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 4.7122 Å / Origin y: -1.3808 Å / Origin z: -2.1595 Å
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Refinement TLS group |
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