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Yorodumi- PDB-2cen: P1' Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cen | ||||||
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Title | P1' Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol in the Transition-State Mimicking Scaffold | ||||||
Components | POL PROTEIN | ||||||
Keywords | HYDROLASE / HIV-1 / PROTEASE / INHIBITOR / ASPARTYL PROTEASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Ginman, N. / Ekegren, J.K. / Johansson, A. / Wallberg, H. / Larhed, M. / Samuelsson, B. / Hallberg, A. / Unge, T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Microwave-Accelerated Synthesis of P1'-Extended HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol in the Transition-State Mimicking Scaffold. Authors: Ekegren, J.K. / Ginman, N. / Johansson, A. / Wallberg, H. / Larhed, M. / Samuelsson, B. / Unge, T. / Hallberg, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS REPRESENTED BY AN 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 | 2cen.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cen.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 2cen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/2cen ftp://data.pdbj.org/pub/pdb/validation_reports/ce/2cen | HTTPS FTP |
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-Related structure data
Related structure data | 2cejC 2cemC 1ebwS 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 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH INHIBITOR AHA478 / Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: HIV-1 D10 / Variant: D10 / Plasmid: PET11D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA References: UniProt: Q8Q3H0, UniProt: Q5RZ09*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-4AH / {( | #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: 2.75 Å3/Da / Density % sol: 54.97 % |
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Crystal grow | pH: 5 Details: 0.7 M NACL, 50 MM MESHCL, 14 MM BME, PH5.0, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.2 Å / Num. obs: 26399 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EBW Resolution: 1.7→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 40.7437 Å2 / ksol: 0.379795 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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Xplor file |
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