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Yorodumi- PDB-2wkz: HIV-1 Protease Inhibitors Containing a Tertiary Alcohol in the Tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wkz | ||||||
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Title | HIV-1 Protease Inhibitors Containing a Tertiary Alcohol in the Transition-State Mimic with Improved Cell-Based Antiviral Activity | ||||||
Components | PROTEASE | ||||||
Keywords | HYDROLASE / TRANSITION-STATE MIMIC / INHIBITOR | ||||||
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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mahalingam, A.K. / Axelsson, L. / Ekegren, J.K. / Wannberg, J. / Kihlstrom, J. / Wallberg, H. / Samuelsson, B. / Larhed, M. / Hallberg, A. / Unge, T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: HIV-1 Protease Inhibitors with a Transition-State Mimic Comprising a Tertiary Alcohol: Improved Antiviral Activity in Cells. Authors: Mahalingam, A.K. / Axelsson, L. / Ekegren, J.K. / Wannberg, J. / Kihlstr, J. / Unge, T. / Wallberg, H. / Samuelsson, B. / Larhed, M. / Hallberg, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wkz.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wkz.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/2wkz ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wkz | HTTPS FTP |
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-Related structure data
Related structure data | 2wl0C 1d4jS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: RESIDUES 501-599 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH INHIBITOR COMPOUND AHA599 Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (Z2/CDC-Z34 ISOLATE) Variant: GROUP M SUBTYPE D / Plasmid: PEXP5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI References: UniProt: P03366, UniProt: P12499*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-5AH / | #3: 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: 2.7 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 5 Details: PROTEASE 2 MG/ML PRECIPITANT 0.7 M NACL, 100 MM MES PH 5.5 |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 1.06 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Num. obs: 26363 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.2 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D4J Resolution: 1.7→45 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 41.7359 Å2 / ksol: 0.373272 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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