[English] 日本語
![](img/lk-miru.gif)
- PDB-2qd7: HIV-1 Protease Mutant V82A with potent Antiviral inhibitor GRL-98065 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2qd7 | ||||||
---|---|---|---|---|---|---|---|
Title | HIV-1 Protease Mutant V82A with potent Antiviral inhibitor GRL-98065 | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE / HIV-1 protease mutant V82A / protease inhibitor | ||||||
Function / homology | ![]() 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 / establishment of integrated proviral latency / viral penetration into host nucleus ...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 / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.F. / Tie, Y. / Boross, P.I. / Tozser, J. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
![]() | ![]() Title: Potent new antiviral compound shows similar inhibition and structural interactions with drug resistant mutants and wild type HIV-1 protease. Authors: Wang, Y.F. / Tie, Y. / Boross, P.I. / Tozser, J. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 107.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 822.5 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qciC ![]() 2qd6C ![]() 2qd8C ![]() 2z4oC ![]() 2idwS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10712.623 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A, V82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 229 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/065.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/065.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-065 / ( | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 25mM citrate phosphate, 10% (w/v) sodium chloride, 6-7% (v/v) dimethylsulfoxide (DMSO), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2003 | |||||||||
Radiation | Monochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.11→50 Å / Num. all: 76186 / Num. obs: 73051 / % possible obs: 97.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 6.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.2 | |||||||||
Reflection shell | Resolution: 1.11→1.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4 / Num. unique all: 5816 / % possible all: 80.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2IDW Resolution: 1.11→10 Å / Num. parameters: 17283 / Num. restraintsaints: 22172 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 22 / Occupancy sum hydrogen: 1623.07 / Occupancy sum non hydrogen: 1736.58 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|