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Yorodumi- PDB-7f9b: Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f9b | ||||||
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Title | Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95 | ||||||
Components | Bifunctional glutamate/proline--tRNA ligase | ||||||
Keywords | LIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / LIGASE / LIGASE-LIGASE INHIBITOR complex | ||||||
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 / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / 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 / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / GAIT complex / RNA stem-loop binding / cellular response to type II interferon / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å | ||||||
Authors | Manickam, Y. / Malhotra, N. / Sharma, A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2023 Title: Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis. Authors: Yogavel, M. / Bougdour, A. / Mishra, S. / Malhotra, N. / Chhibber-Goel, J. / Bellini, V. / Harlos, K. / Laleu, B. / Hakimi, M.A. / Sharma, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f9b.cif.gz | 404.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f9b.ent.gz | 326.5 KB | Display | PDB format |
PDBx/mmJSON format | 7f9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/7f9b ftp://data.pdbj.org/pub/pdb/validation_reports/f9/7f9b | HTTPS FTP |
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-Related structure data
Related structure data | 7f98C 7f99C 7f9aC 7f9cC 7f9dC 7fakC 7falC 7famC 7fanC 7vc1C 7vc2C 7vc3C 5vadS 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: 57530.840 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 , 6 types, 280 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | #7: 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: 2.19 Å3/Da / Density % sol: 43.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1 M HEPES, 1.5 M CaCl2, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9799 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 1.995→45.48 Å / Num. obs: 66905 / % possible obs: 98.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.127 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.995→2.11 Å / Rmerge(I) obs: 0.928 / Num. unique obs: 10924 / Rrim(I) all: 1.008 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VAD Resolution: 1.995→45.48 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.9 / 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: 118.53 Å2 / Biso mean: 47.0135 Å2 / Biso min: 26.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.995→45.48 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 5.6991 Å / Origin y: -7.2818 Å / Origin z: 19.0673 Å
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Refinement TLS group | Selection details: all |