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- PDB-1y5x: tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y5x | ||||||
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Title | tRNA-guanine Transglycosylase (TGT) in complex with 6-Amino-4-[2-(4-methoxyphenyl)ethyl]-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one | ||||||
![]() | Queuine tRNA-ribosyltransferase![]() | ||||||
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Function / homology | ![]() tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G. | ||||||
![]() | ![]() Title: Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding Authors: Stengl, B. / Meyer, E.A. / Heine, A. / Brenk, R. / Diederich, F. / Klebe, G. #1: ![]() Title: Synthesis, Biological Evaluation and Crystallographic Studies of Extended Guanine-based (lin-Benzoguanine) Inhibitors for tRNA-Guanine Transglycosylase (TGT) Authors: Meyer, E.A. / Donati, N. / Guillot, M. / Schweizer, B. / Diederich, F. / Stengl, B. / Heine, A. / Brenk, R. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160 KB | Display | ![]() |
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PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1y5vC ![]() 1y5wC ![]() 2bbfC ![]() 1p0dS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 42794.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG8000, MES, DMSO, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 7, 2003 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→20 Å / Num. all: 44873 / Num. obs: 44873 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2269 / Rsym value: 0.357 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1P0D Resolution: 2.1→19.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 530934.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.2191 Å2 / ksol: 0.369198 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Xplor file |
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