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Yorodumi- PDB-1kjh: SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kjh | ||||||
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Title | SUBSTRATE SHAPE DETERMINES SPECIFICITY OF RECOGNITION RECOGNITION FOR HIV-1 PROTEASE: ANALYSIS OF CRYSTAL STRUCTURES OF SIX SUBSTRATE COMPLEXES | ||||||
Components | (POL POLYPROTEIN) x 2 | ||||||
Keywords | HYDROLASE / RNASE H / INTEGRASE / 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 / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kjh.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kjh.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kjh_validation.pdf.gz | 386.5 KB | Display | wwPDB validaton report |
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Full document | 1kjh_full_validation.pdf.gz | 388.6 KB | Display | |
Data in XML | 1kjh_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1kjh_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/1kjh ftp://data.pdbj.org/pub/pdb/validation_reports/kj/1kjh | HTTPS FTP |
-Related structure data
Related structure data | 1kj4C 1kj7C 1kjfC 1kjgC 1f7aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin #2: Protein/peptide | | Mass: 1189.491 Da / Num. of mol.: 1 Fragment: RNASE H-INTEGRASE SUBSTRATE PEPTIDE, RESIDUES 723-732 Source method: obtained synthetically / References: UniProt: P03368, UniProt: P03366*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: AMMONIUM SULPHATE, SODIUM CITRATE, SODIUM PHOSPHATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 25, 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→32.85 Å / Num. all: 12905 / Num. obs: 12905 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.5 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1F7A Resolution: 2→32.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 164979.87 / 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: 63.3476 Å2 / ksol: 0.349263 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.85 Å
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Refine LS restraints |
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Xplor file |
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