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Yorodumi- PDB-1a9m: G48H MUTANT OF HIV-1 PROTEASE IN COMPLEX WITH A PEPTIDIC INHIBITO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a9m | ||||||
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Title | G48H MUTANT OF HIV-1 PROTEASE IN COMPLEX WITH A PEPTIDIC INHIBITOR U-89360E | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | ASPARTYL PROTEASE / DRUG RESISTANT / MUTATION | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / 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 ...symbiont-mediated activation of host apoptosis / 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 / 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 / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hong, L. / Zhang, X.-J. / Foundling, S. / Hartsuck, J.A. / Tang, J. | ||||||
Citation | Journal: FEBS Lett. / Year: 1997 Title: Structure of a G48H mutant of HIV-1 protease explains how glycine-48 replacements produce mutants resistant to inhibitor drugs. Authors: Hong, L. / Zhang, X.J. / Foundling, S. / Hartsuck, J.A. / Tang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a9m.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a9m.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a9m_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 1a9m_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 1a9m_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1a9m_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/1a9m ftp://data.pdbj.org/pub/pdb/validation_reports/a9/1a9m | HTTPS FTP |
-Related structure data
Related structure data | 1gnoS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.41715, -0.74841, 0.51562), Vector: |
-Components
#1: Protein | Mass: 10884.852 Da / Num. of mol.: 2 / Mutation: G48H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: PET3B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03368, UniProt: P03366*PLUS #2: Chemical | ChemComp-U0E / | #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: 2.8 Å3/Da / Density % sol: 55.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.8 Details: THE PROTEIN SOLUTION CONTAINED 6.5 MG/ML MUTANT HIV-1 PROTEASE IN 20 MM SODIUM ACETATE, 1 MM DITHIOTHREITOL, PH 5.5, WITH A 10-FOLD MOLAR EXCESS OF INHIBITOR. THE RESERVOIR SOLUTIONS FOR THE ...Details: THE PROTEIN SOLUTION CONTAINED 6.5 MG/ML MUTANT HIV-1 PROTEASE IN 20 MM SODIUM ACETATE, 1 MM DITHIOTHREITOL, PH 5.5, WITH A 10-FOLD MOLAR EXCESS OF INHIBITOR. THE RESERVOIR SOLUTIONS FOR THE VAPOR DIFFUSION CONTAINED 10% DIMETHYLSULFOXIDE, 30 MM B-MERCAPTOETHANOL AND 4% 2-PROPANOL IN ADDITION TO THE PRECIPITANT. THE MOST FAVORABLE CRYSTALLIZATION CONDITIONS WERE 42% SATURATED AMMONIUM SULFATE, PH 6.8., vapor diffusion PH range: 5.5-6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1996 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 8697 / % possible obs: 78 % / Redundancy: 3 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.073 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3 / Rsym value: 0.32 / % possible all: 52.6 |
Reflection | *PLUS Num. measured all: 25380 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 52.6 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GNO Resolution: 2.3→8 Å
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Displacement parameters | Biso mean: 36.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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