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- PDB-1mt9: Viability of a drug-resistant HIV-1 protease mutant: structural i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mt9 | ||||||
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Title | Viability of a drug-resistant HIV-1 protease mutant: structural insights for better antiviral therapy | ||||||
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![]() | HYDROLASE/HYDROLASE SUBSTRATE / Matrix / Capsid / Gag cleavage / drug resistance / substrate recognition / HYDROLASE / HYDROLASE-HYDROLASE SUBSTRATE 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 | ![]() ![]() | ||||||
![]() | Prabu-Jeyabalan, M. / Nalivaika, E.A. / King, N.M. / Schiffer, C.A. | ||||||
![]() | ![]() Title: Viability of drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy Authors: Prabu-Jeyabalan, M. / Nalivaika, E.A. / King, N.M. / Schiffer, C.A. #1: ![]() Title: How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease Authors: Prabu-Jeyabalan, M. / Nalivaika, E.A. / Schiffer, C.A. #2: ![]() Title: Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes Authors: Prabu-Jeyabalan, M. / Nalivaika, E.A. / Schiffer, C.A. #3: ![]() Title: Lack of synergy for inhibitors targeting a multi-drug resistant HIV-1 protease Authors: King, N.M. / Melnick, L. / Prabu-Jeyabalan, M. / Nalivaika, E.A. / Yang, S.-S. / Gao, Y. / Nie, X. / Zepp, C. / Heefner, D.L. / Schiffer, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
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PDB format | ![]() | 39.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 388.2 KB | Display | ![]() |
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Full document | ![]() | 390.8 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mt7C ![]() 1mt8C ![]() 1mtbC ![]() 1n49C ![]() 1mtrS 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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1 |
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Unit cell |
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Details | The entire dimer is provided in the coordinate set and the monomers are distinguished by the chain IDs `A' and `B'. The decamer sequence corresponding to the MA-CA cleavage site of HIV-1 Gag polyprotein. |
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Components
#1: Protein | Mass: 10772.724 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, L63P, V82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | | Mass: 1173.325 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This peptide sequence occurs naturally in Gag of HIV-1 #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.41 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: sodium phosphate, sodium citrate, ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 30, 1999 / Details: Yale mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.84 Å / Num. all: 12659 / Num. obs: 12659 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.33 / Num. unique all: 1182 / % possible all: 92 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 98506 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 92 % / Num. unique obs: 1182 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MTR Resolution: 2→32.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 172172.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.3885 Å2 / ksol: 0.367432 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å |