+Open data
-Basic information
Entry | Database: PDB / ID: 2a1e | ||||||
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Title | High resolution structure of HIV-1 PR with TS-126 | ||||||
Components | Pol polyprotein | ||||||
Keywords | HYDROLASE / HIV PR / PEPTIDOMIMETIC INHIBITOR / STEREOISOMER / SCREENING A MIXTURE | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Demitri, N. / Geremia, S. / Randaccio, L. / Wuerges, J. / Benedetti, F. / Berti, F. / Dinon, F. / Campaner, P. / Tell, G. | ||||||
Citation | Journal: Chemmedchem / Year: 2006 Title: A potent HIV protease inhibitor identified in an epimeric mixture by high-resolution protein crystallography. Authors: Geremia, S. / Demitri, N. / Wuerges, J. / Benedetti, F. / Berti, F. / Tell, G. / Randaccio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a1e.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a1e.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a1e_validation.pdf.gz | 818.8 KB | Display | wwPDB validaton report |
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Full document | 2a1e_full_validation.pdf.gz | 821.3 KB | Display | |
Data in XML | 2a1e_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 2a1e_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/2a1e ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a1e | HTTPS FTP |
-Related structure data
Related structure data | 1s6g 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 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 / Fragment: Protease / Mutation: Q7K/L33I/L63I/C67A/C95A Source method: isolated from a genetically manipulated source Details: IPF: Pseudo-esapeptide built up from a di-hydroxyethylene Phe-Pro isostere core, coupled with 2 equivalents of Ac-NH-Trp-Val-OH. Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: GAG-POL / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin |
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-Non-polymers , 7 types, 283 molecules
#2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Chemical | ChemComp-IPF / | #7: Chemical | ChemComp-GOL / | #8: 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: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, DMSO, sodium acetate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 / Wavelength: 1.2 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 3, 2004 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.3→10 Å / Num. all: 55106 / Num. obs: 55106 / % possible obs: 98.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10 | |||||||||
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S6G 1s6g Resolution: 1.3→10 Å / Num. parameters: 15541 / Num. restraintsaints: 18509 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.3%
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Displacement parameters | Biso mean: 19.49 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 1679 / Occupancy sum non hydrogen: 1849 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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