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Yorodumi- PDB-2aoe: crystal structure analysis of HIV-1 protease mutant V82A with a s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aoe | ||||||
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Title | crystal structure analysis of HIV-1 protease mutant V82A with a substrate analog CA-P2 | ||||||
Components | POL POLYPROTEIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / SUBSTRATE ANALOG / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information RNA stem-loop binding / host cell / 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 ...RNA stem-loop binding / host cell / 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 / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Liu, F. / Chen, X. / Tozser, J. / Harrison, R.W. / Weber, I.T. | ||||||
Citation | Journal: Febs J. / Year: 2005 Title: Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs. Authors: Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Liu, F. / Chen, X. / Tozser, J. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aoe.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aoe.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 2aoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/2aoe ftp://data.pdbj.org/pub/pdb/validation_reports/ao/2aoe | HTTPS FTP |
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-Related structure data
Related structure data | 2aocC 2aodC 2aofC 2aogC 2aohC 2aoiC 2aojC 1dazS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10712.623 Da / Num. of mol.: 2 / Fragment: PROTEASE (RETROPEPSIN) / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (BH5 ISOLATE) Genus: Lentivirus / Species: Human immunodeficiency virus 1Subtypes of HIV / Strain: BH5 isolate / Gene: POL / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04587, HIV-1 retropepsin |
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-Non-polymers , 7 types, 204 molecules
#2: Chemical | ChemComp-NA / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-ACY / | #6: Chemical | #7: Chemical | ChemComp-0Q4 / | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H70N11O8 References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide #8: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | THE INHIBITOR 0Q4 WAS CHEMICALLY SYNTHESIZED AND IS ANALOGOUS TO THE CA-P2 PROCESSING SITE ...THE INHIBITOR 0Q4 WAS CHEMICALLY |
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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: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: SODIUM CHLORIDE 1.3M, DMSO 7%,SODIUM ACETATE BUFFER, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. all: 34681 / % possible obs: 99.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.54→1.6 Å / Rmerge(I) obs: 0.371 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1DAZ Resolution: 1.54→10 Å / Num. parameters: 17888 / Num. restraintsaints: 23414 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 35 / Occupancy sum hydrogen: 1657.04 / Occupancy sum non hydrogen: 1728.71 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→10 Å
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Refine LS restraints |
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