+Open data
-Basic information
Entry | Database: PDB / ID: 1kzk | ||||||
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Title | JE-2147-HIV Protease Complex | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV Protease Complex / Anisotropic Displacement Parameters / Viral protein / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Reiling, K.K. / Endres, N.F. / Dauber, D.S. / Craik, C.S. / Stroud, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Anisotropic Dynamics of the JE-2147-HIV Protease Complex: Drug Resistance and Thermodynamic Binding Mode Examined in a 1.09 A Structure Authors: Reiling, K.K. / Endres, N.F. / Dauber, D.S. / Craik, C.S. / Stroud, R.M. #1: Journal: J.Med.Chem. / Year: 1999 Title: Structure-Activity Relationship of Small-Sized HIV Protease Inhibitors Containing Allophenylnorstatine Authors: Mimoto, T. / Kato, R. / Takaku, H. / Nojima, S. / Terashima, K. / Misawa, S. / Fukazawa, T. / Ueno, T. / Sato, H. / Shintani, M. / Kiso, Y. / Hayashi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kzk.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kzk.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kzk ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzk | HTTPS FTP |
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-Related structure data
Related structure data | 1hpxS S: Starting model for refinement |
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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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Details | The Protease is active as a Dimer |
-Components
#1: Protein | Mass: 10801.763 Da / Num. of mol.: 2 / Mutation: Q7K, K14R, S37N, R41K, L63P, I64V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus / Genus: Lentivirus / Plasmid: pTacTac / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin #2: Chemical | ChemComp-JE2 / ( | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #5: 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: 2.18 Å3/Da / Density % sol: 43.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: NaAc, NaCl, EDTA, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 2000 |
Radiation | Monochromator: single crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→42.64 Å / Num. all: 79223 / Num. obs: 79223 / % possible obs: 93.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.09→1.11 Å / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.1 / % possible all: 61.8 |
Reflection | *PLUS Highest resolution: 1.09 Å / Lowest resolution: 42.64 Å / % possible obs: 93.4 % / Num. measured all: 433956 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS Lowest resolution: 3.15 Å / % possible obs: 61.8 % / Rmerge(I) obs: 0.753 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Poly Serine PDB ENTRY 1HPX Resolution: 1.09→6 Å / Num. parameters: 16580 / Num. restraintsaints: 21599 / Cross valid method: Free-R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 12.9 Å2 | |||||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 1506.94 / Occupancy sum non hydrogen: 1771.55 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→6 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |