[English] 日本語
Yorodumi- PDB-1kj7: SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kj7 | ||||||
---|---|---|---|---|---|---|---|
Title | SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES | ||||||
Components |
| ||||||
Keywords | HYDROLASE / p2-Nucleocapsid / SUBSTRATE RECOGNITION | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Schiffer, C.A. | ||||||
Citation | Journal: Structure / Year: 2002 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kj7.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kj7.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/1kj7 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/1kj7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kj4C 1kjfC 1kjgC 1kjhC 1f7aS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin #2: Protein/peptide | | Mass: 1119.338 Da / Num. of mol.: 1 Fragment: P2-NUCLEOCAPSID SUBSTRATE PEPTIDE, RESIDUES 372-381 Source method: obtained synthetically / References: UniProt: P20875 #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.81 % |
---|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 24, 2000 / 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→32.93 Å / Num. all: 12913 / Num. obs: 12913 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.7 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1F7A Resolution: 2→32.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 242009.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 76.3328 Å2 / ksol: 0.359898 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.6 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.93 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|