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- PDB-1kjg: SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kjg | ||||||
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Title | SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES | ||||||
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Function / homology | ![]() RNA stem-loop binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schiffer, C.A. | ||||||
![]() | ![]() Title: Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Authors: Prabu-Jeyabalan, M. / Nalivaika, E. / Schiffer, C.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 | ![]() | 55.4 KB | Display | ![]() |
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PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kj4C ![]() 1kj7C ![]() 1kjfC ![]() 1kjhC ![]() 1f7aS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10800.777 Da / Num. of mol.: 2 / Fragment: HIV-1 PROTEASE, RESIDUES 57-155 / Mutation: D25N,Q7K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | | ![]() Mass: 1029.058 Da / Num. of mol.: 1 Fragment: REVERSE TRANSRIPTASE-RNASE H SUBSTRATE PEPTIDE, RESIDUES 436-445 Source method: obtained synthetically / References: ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.37 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: AMMONIUM SULPHATE, SODIUM PHOSPHATE, SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 9, 2000 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→32.79 Å / Num. all: 13019 / Num. obs: 13019 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1F7A Resolution: 2→32.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 123602.47 / 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: 67.0507 Å2 / ksol: 0.357341 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.79 Å
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Refine LS restraints |
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Xplor file |
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