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Yorodumi- PDB-7y28: Controlling fibrosis using compound with novel binding mode to pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y28 | ||||||
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Title | Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1 | ||||||
Components | Bifunctional glutamate/proline--tRNA ligase | ||||||
Keywords | TRANSLATION / prolyl-trna synthetase / inhibitor / fibrosis / binding mode | ||||||
Function / homology | Function and homology information regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / glutamyl-tRNA aminoacylation / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / aminoacyl-tRNA synthetase multienzyme complex / GAIT complex / cellular response to type II interferon / RNA stem-loop binding / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Kim, S. / Yoon, I. / Son, J. / Park, S. / Hwang, K.Y. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Embo Mol Med / Year: 2023 Title: Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1. Authors: Yoon, I. / Kim, S. / Cho, M. / You, K.A. / Son, J. / Lee, C. / Suh, J.H. / Bae, D.J. / Kim, J.M. / Oh, S. / Park, S. / Kim, S. / Cho, S.H. / Park, S. / Bang, K. / Seo, M. / Kim, J.H. / Lee, ...Authors: Yoon, I. / Kim, S. / Cho, M. / You, K.A. / Son, J. / Lee, C. / Suh, J.H. / Bae, D.J. / Kim, J.M. / Oh, S. / Park, S. / Kim, S. / Cho, S.H. / Park, S. / Bang, K. / Seo, M. / Kim, J.H. / Lee, B. / Park, J.S. / Hwang, K.Y. / Kim, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y28.cif.gz | 212 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y28.ent.gz | 165.9 KB | Display | PDB format |
PDBx/mmJSON format | 7y28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y28_validation.pdf.gz | 4.3 MB | Display | wwPDB validaton report |
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Full document | 7y28_full_validation.pdf.gz | 4.3 MB | Display | |
Data in XML | 7y28_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 7y28_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/7y28 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/7y28 | HTTPS FTP |
-Related structure data
Related structure data | 7y1hC 7y1wC 7y3sC 4k88S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56618.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 / Production host: Escherichia coli (E. coli) References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase |
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-Non-polymers , 5 types, 142 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #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: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3500, CaCl2 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→45.43 Å / Num. obs: 45110 / % possible obs: 93.84 % / Redundancy: 4.5 % / Biso Wilson estimate: 38.26 Å2 / CC1/2: 0.749 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.29→2.33 Å / Num. unique obs: 45110 / CC1/2: 0.749 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K88 Resolution: 2.29→45.43 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 29.34 / 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: 160.74 Å2 / Biso mean: 52.0221 Å2 / Biso min: 14.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→45.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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