+Open data
-Basic information
Entry | Database: PDB / ID: 7ueo | |||||||||
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Title | PANK3 complex structure with compound PZ-3977 | |||||||||
Components | Pantothenate kinase 3 | |||||||||
Keywords | TRANSFERASE / PANK / Substrate / Complex / Pantothenate kinase / Inhibitor / Activator | |||||||||
Function / homology | Function and homology information Coenzyme A biosynthesis / vitamin binding / acetyl-CoA binding / pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / protein homodimerization activity / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | White, S.W. / Yun, M. / Lee, R.E. | |||||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Discovery of hPANK Activators with Improved Pharmacological Properties Authors: Tangallapally, R. / Edwards, A. / Subramanian, C. / Sharma, L.K. / Yun, M. / White, S.W. / Jackowski, S. / Rock, C.O. / Lee, R.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ueo.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ueo.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ueo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ueo_validation.pdf.gz | 961.9 KB | Display | wwPDB validaton report |
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Full document | 7ueo_full_validation.pdf.gz | 964.9 KB | Display | |
Data in XML | 7ueo_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 7ueo_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/7ueo ftp://data.pdbj.org/pub/pdb/validation_reports/ue/7ueo | HTTPS FTP |
-Related structure data
Related structure data | 7ue3C 7ue4C 7ue5C 7ue6C 7ue7C 7uepC 7ueqC 7uerC 7uesC 7uetC 7ueuC 7uevC 7uexC 7ueyC 6b3vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42125.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PANK3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H999, pantothenate kinase |
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-Non-polymers , 5 types, 165 molecules
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-ANP / | ||
#4: Chemical | ChemComp-Y90 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 2.27 Å3/Da / Density % sol: 45.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, ammonium acetate, citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 35644 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 23.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.076 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2195 / CC1/2: 0.857 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B3V Resolution: 1.8→42.39 Å / SU ML: 0.1878 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.2404 / Stereochemistry target values: CDL v1.2
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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 mean: 31.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.39 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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