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- PDB-7f9b: Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-pro... -
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Open data
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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 | ||||||
![]() | Bifunctional glutamate/proline--tRNA ligase | ||||||
![]() | LIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / INHIBITOR / PRS / ATP POCKET / LIGASE / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Manickam, Y. / Malhotra, N. / Sharma, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 404.4 KB | Display | ![]() |
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PDB format | ![]() | 326.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 983.2 KB | Display | ![]() |
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Full document | ![]() | 990.6 KB | Display | |
Data in XML | ![]() | 37 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: P07814, glutamate-tRNA ligase, proline-tRNA ligase |
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-Non-polymers , 6 types, 280 molecules ![](data/chem/img/JE6.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |