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- PDB-1k2b: Combining Mutations in HIV-1 Protease to Understand Mechanisms of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k2b | ||||||
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Title | Combining Mutations in HIV-1 Protease to Understand Mechanisms of Resistance | ||||||
![]() | PROTEASE RETROPEPSIN | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Mahalingam, B. / Boross, P. / Wang, Y.-F. / Louis, J.M. / Fischer, C. / Tozser, J. / W Harrison, R. / Weber, I.T. | ||||||
![]() | ![]() Title: Combining mutations in HIV-1 protease to understand mechanisms of resistance. Authors: Mahalingam, B. / Boross, P. / Wang, Y.F. / Louis, J.M. / Fischer, C.C. / Tozser, J. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.6 KB | Display | ![]() |
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PDB format | ![]() | 40 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 974.8 KB | Display | ![]() |
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Full document | ![]() | 980.6 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k1tC ![]() 1k1uC ![]() 1k2cC ![]() 1dazS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10759.699 Da / Num. of mol.: 2 / Mutation: Q7K, l33I, L63I, C67A, C95A, N88D, L90M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-0Q4 / | ![]() References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR 0Q4 WAS CHEMICALLY SYNTHESIZED AND IS ANALOGOUS TO THE CA-P2 PROCESSING SITE ...THE INHIBITOR 0Q4 WAS CHEMICALLY | Sequence details | MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM ...MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM AUTOPROTEO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.08 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20-50% Saturated Ammonium Sulphate, 10% DMSO, 0.25M citrate/0.5M phosphate buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 6.5 / PH range high: 5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999 |
Radiation | Monochromator: Double-crystal, fixed-exit Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.037 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. all: 20000 / Num. obs: 20000 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1958 / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 8 Å / % possible obs: 99 % / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS Rmerge(I) obs: 0.248 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DAZ Resolution: 1.7→8 Å / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å
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Refinement | *PLUS Rfactor Rfree: 0.275 / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Rfactor Rfree: 0.3784 / Rfactor Rwork: 0.3196 |