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Yorodumi- PDB-1mtb: Viability of a drug-resistant HIV-1 protease mutant: structural i... -
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-Basic information
Entry | Database: PDB / ID: 1mtb | |||||||||
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Title | Viability of a drug-resistant HIV-1 protease mutant: structural insights for better antiviral therapy | |||||||||
Components | PROTEASE RETROPEPSIN | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / drug resistance / substrate recognition / inhibitor binding / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information 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 / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 | Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | |||||||||
Authors | Prabu-Jeyabalan, M. / Nalivaika, E.A. / King, N.M. / Schiffer, C.A. | |||||||||
Citation | Journal: J.Virol. / Year: 2003 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: Journal: J.Mol.Biol. / Year: 2000 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: Journal: Structure / Year: 2002 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: Journal: Protein Sci. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mtb.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mtb.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mtb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mtb_validation.pdf.gz | 471.1 KB | Display | wwPDB validaton report |
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Full document | 1mtb_full_validation.pdf.gz | 475.3 KB | Display | |
Data in XML | 1mtb_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1mtb_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/1mtb ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mtb | HTTPS FTP |
-Related structure data
Related structure data | 1mt7C 1mt8C 1mt9C 1n49C 1f7aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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' + RO 31-8959 (HIV-1 PROTEASE INHIBITOR SAQUINAVIR) |
-Components
#1: Protein | Mass: 10799.727 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, L63P, V82A Source method: isolated from a genetically manipulated source Details: complexed with SAQUINAVIR, RO 31-8959; FDA APPROVED HIV-1 PROTEASE INHIBITOR Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pXC35-pEN18 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin #2: Chemical | ChemComp-ROC / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % | ||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 8, 2001 / 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: 2.5→26.6 Å / Num. all: 6743 / Num. obs: 6743 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.33 / Num. unique all: 496 / % possible all: 71 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 28072 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 71 % / Num. unique obs: 496 / Rmerge(I) obs: 0.36 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1F7A Resolution: 2.5→26.56 Å / Rfactor Rfree error: 0.01 / 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: 57.0169 Å2 / ksol: 0.339017 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.41 Å / Luzzati sigma a free: 0.53 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→26.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rwork: 0.3 |