+Open data
-Basic information
Entry | Database: PDB / ID: 2azc | ||||||
---|---|---|---|---|---|---|---|
Title | HIV-1 Protease NL4-3 6X mutant | ||||||
Components | PROTEASE RETROPEPSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV / protease / inhibitor / TL-3 / 6X / 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 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Heaslet, H. / Kutilek, V. / Morris, G.M. / Lin, Y.-C. / Elder, J.H. / Torbett, B.E. / Stout, C.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3 Authors: Heaslet, H. / Kutilek, V. / Morris, G.M. / Lin, Y.-C. / Elder, J.H. / Torbett, B.E. / Stout, C.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2azc.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2azc.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 2azc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/2azc ftp://data.pdbj.org/pub/pdb/validation_reports/az/2azc | HTTPS FTP |
---|
-Related structure data
Related structure data | 2az8SC 2az9C 2azbC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10749.708 Da / Num. of mol.: 2 / Mutation: L24I,M46I,F53L,L63P,V77I,V82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: R8 / Description: Protease NL4-3 / Gene: pol / Plasmid: pET 21a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3, pLys S / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE. THE STRUCTURE WAS REFINED WITH HALF OF THE C2 ...THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE. THE STRUCTURE WAS REFINED WITH HALF OF THE C2 SYMMETRIC LIGAND 3TL IN THE ASYMMETRIC | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % |
---|---|
Crystal grow | Temperature: 297.16 K / pH: 5.2 Details: ammonium sulfate, sodium acetate, sodium thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 297.16K, pH 5.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5419 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 19, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→34.88 Å / Num. obs: 16751 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4.84 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8 |
-Phasing
Phasing MR | Rfactor: 0.492 / Cor.coef. Fo:Fc: 0.432
|
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AZ8 Resolution: 2.01→34.88 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→34.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|