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- PDB-1kj4: SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kj4 | ||||||
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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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![]() | HYDROLASE / MARIX-CAPSID / SUBSTRATE RECOGNITION | ||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.2 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.8 KB | Display | ![]() |
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Full document | ![]() | 428.8 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kj7C ![]() 1kjfC ![]() 1kjgC ![]() 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | THE ENTIRE BIOLOGICAL DIMER ALONG WITH THE SUBSTRATE PEPTIDE BOUND IN THE ACTIVE SITE ARE PROVIDED IN THIS COORDINATE FILE |
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Components
#1: Protein | Mass: 10800.777 Da / Num. of mol.: 4 / 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: 1161.264 Da / Num. of mol.: 2 / Fragment: MATRIX-CAPSID SUBSTRATE PEPTIDE, RESIDUES 127-136 / Source method: obtained synthetically / References: UniProt: P20875 #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.88 % |
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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: Aug 26, 1999 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→38.88 Å / Num. all: 12376 / Num. obs: 12376 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 4.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F7A Resolution: 2.9→38.88 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 64173.54 / 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: 69.2161 Å2 / ksol: 0.341402 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→38.88 Å
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Refine LS restraints |
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Xplor file |
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