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Yorodumi- PDB-2aog: Crystal structure analysis of HIV-1 protease mutant V82A with a s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aog | ||||||
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Title | Crystal structure analysis of HIV-1 protease mutant V82A with a substrate analog P2-NC | ||||||
Components | HIV-1 PROTEASE (RETROPEPSIN) | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / MUTANT / DIMER / SUBSTRATE ANALOG / 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 / 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: 1.1 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 | 2aog.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aog.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 2aog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/2aog ftp://data.pdbj.org/pub/pdb/validation_reports/ao/2aog | HTTPS FTP |
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-Related structure data
Related structure data | 2aocC 2aodSC 2aoeC 2aofC 2aohC 2aoiC 2aojC 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 / Mutation: Q7K, L33I, L63I, C67A, V82A, C95A 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 , 5 types, 276 molecules
#2: Chemical | ChemComp-2NC / | ||||
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#3: Chemical | ChemComp-UNX / | ||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACY / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | IN THE DEPOSITED FILE, THE INHIBITOR 2NC HAD AN EXTRA O7 ATOM IN CONFORMATION B WHICH ACCORDING TO ...IN THE DEPOSITED FILE, THE INHIBITOR 2NC HAD AN EXTRA O7 ATOM IN CONFORMATI |
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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: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: SODIUM CHLORIDE 0.4M, DMSO 5%,CITRATE PHOSPHATE BUFFER, pH 5.4, 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: 0.92 / Wavelength: 0.92 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2003 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→50 Å / Num. all: 95318 / % possible obs: 94.8 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.4 | |||||||||
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / % possible all: 68.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2AOD Resolution: 1.1→10 Å / Num. parameters: 18897 / Num. restraintsaints: 25007 / 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: 45 / Occupancy sum hydrogen: 1652.1 / Occupancy sum non hydrogen: 1808.44 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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