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Yorodumi- PDB-2aod: Crystal structure analysis of HIV-1 protease with a substrate ana... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aod | ||||||
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Title | Crystal structure analysis of HIV-1 protease with a substrate analog P2-NC | ||||||
Components | HIV-1 PROTEASE | ||||||
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 / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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: 1.4 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 | 2aod.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aod.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 2aod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aod_validation.pdf.gz | 733.3 KB | Display | wwPDB validaton report |
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Full document | 2aod_full_validation.pdf.gz | 736.2 KB | Display | |
Data in XML | 2aod_validation.xml.gz | 13 KB | Display | |
Data in CIF | 2aod_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/2aod ftp://data.pdbj.org/pub/pdb/validation_reports/ao/2aod | HTTPS FTP |
-Related structure data
Related structure data | 2aocSC 2aoeC 2aofC 2aogC 2aohC 2aoiC 2aojC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, 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 1 / 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, 205 molecules
#2: Chemical | ChemComp-DMS / | ||
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#3: Chemical | ChemComp-UNX / | ||
#4: Chemical | ChemComp-2NC / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | ACCORDING TO THE AUTHORS THE ATOM MARKED AS UNX IN THE COORDINATES IS AN IMPURITY OBSERVED IN THE ...ACCORDING TO THE AUTHORS THE ATOM MARKED AS UNX IN THE COORDINATE |
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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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: AMMONIUM SULFATE 17%, CITRATE PHOSPHATE BUFFER PH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 7, 2003 |
Radiation | Monochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 46637 / % possible obs: 95.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.06 / % possible all: 66.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2AOC Resolution: 1.4→10 Å / Num. parameters: 16976 / Num. restraintsaints: 21445 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 23 / Occupancy sum hydrogen: 1663 / Occupancy sum non hydrogen: 1765.03 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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