+Open data
-Basic information
Entry | Database: PDB / ID: 7ue3 | ||||||
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Title | PANK3 complex structure with compound PZ-3804 | ||||||
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: 1.56 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 | 7ue3.cif.gz | 190.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ue3.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ue3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/7ue3 ftp://data.pdbj.org/pub/pdb/validation_reports/ue/7ue3 | HTTPS FTP |
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-Related structure data
Related structure data | 7ue4C 7ue5C 7ue6C 7ue7C 7ueoC 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, 230 molecules
#2: Chemical | ChemComp-ND6 / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #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: 2.29 Å3/Da / Density % sol: 46.18 % |
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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: Aug 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→50 Å / Num. obs: 55022 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.56→1.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3354 / CC1/2: 0.805 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B3V Resolution: 1.56→32.14 Å / SU ML: 0.1448 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.4439 / 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: 26.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→32.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -30.0500337031 Å / Origin y: -7.84762309837 Å / Origin z: 5.28865163031 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 11 through 369) |