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- PDB-7f99: 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: 7f99 | ||||||
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Title | Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96 | ||||||
![]() | Bifunctional glutamate/proline--tRNA ligase | ||||||
![]() | LIGASE/LIGASE INHIBITOR / PROTEIN TRANSLATION / MALARIA / INHIBITOR / PRS / 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 | ![]() | 417.3 KB | Display | ![]() |
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PDB format | ![]() | 337.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.2 MB | Display | ![]() |
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Full document | ![]() | 4.2 MB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 56.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f98C ![]() 7f9aC ![]() 7f9bC ![]() 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, 420 molecules ![](data/chem/img/1UI.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: 43.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 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 EIGER2 X 16M / Detector: PIXEL / Date: May 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.979→78.252 Å / Num. obs: 69229 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.121 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 6.6 % / Num. unique obs: 3404 / CC1/2: 0.5 / Rrim(I) all: 0.854 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VAD Resolution: 1.979→78.252 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 25.61 / 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: 111.81 Å2 / Biso mean: 43.1434 Å2 / Biso min: 16.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.979→78.252 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: 5.9905 Å / Origin y: -6.8841 Å / Origin z: 18.5215 Å
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Refinement TLS group | Selection details: all |