+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ec2 | ||||||
---|---|---|---|---|---|---|---|
Title | HIV-1 protease in complex with the inhibitor BEA428 | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Dimer / protein-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 | ![]() ![]() | ||||||
![]() | Unge, T. | ||||||
![]() | ![]() Title: Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors Authors: Andersson, H.O. / Fridborg, K. / Lowgren, S. / Alterman, M. / Muhlman, A. / Bjorsne, M. / Garg, N. / Kvarnstrom, I. / Schaal, W. / Classon, B. / Karlen, A. / Danielsson, U.H. / Ahlsen, G. / ...Authors: Andersson, H.O. / Fridborg, K. / Lowgren, S. / Alterman, M. / Muhlman, A. / Bjorsne, M. / Garg, N. / Kvarnstrom, I. / Schaal, W. / Classon, B. / Karlen, A. / Danielsson, U.H. / Ahlsen, G. / Nillroth, U. / Vrang, L. / Oberg, B. / Samuelsson, B. / Hallberg, A. / Unge, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1d4hC ![]() 1d4iC ![]() 1d4jC ![]() 1ebwC ![]() 1ebyC ![]() 1ebzC ![]() 1ec1C ![]() 1ec3C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer |
-
Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: FRAGMENT 69-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-BEJ / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.4 M Sodium chloride, 0.05 M MES, 0.02 % (W/V) sodium azide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Details: used microseeding | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 26, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.958 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.76 Å / Num. all: 16587 / Num. obs: 15012 / % possible obs: 90.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.02 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.39 / Num. unique all: 2336 / % possible all: 90.1 |
Reflection | *PLUS Num. obs: 15612 / % possible obs: 92.9 % / Num. measured all: 44926 / Rmerge(I) obs: 0.116 |
Reflection shell | *PLUS Lowest resolution: 2.07 Å |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→24.76 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1356235.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: Refined with CNS program system
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.6 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.2 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.76 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 24.7 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.207 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.25 |