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Yorodumi- PDB-1ff0: STRUCTURAL IMPLICATIONS OF DRUG RESISTANT MUTANTS OF HIV-1 PROTEA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ff0 | ||||||
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Title | STRUCTURAL IMPLICATIONS OF DRUG RESISTANT MUTANTS OF HIV-1 PROTEASE: HIGH RESOLUTION CRYSTAL STRUCTURES OF THE MUTANT PROTEASE/SUBSTRATE ANALOG COMPLEXES. | ||||||
Components | PROTEASE RETROPEPSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / 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 / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å | ||||||
Authors | Mahalingam, B. / Louis, J.M. / Harrison, R.W. / Weber, I.T. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes. Authors: Mahalingam, B. / Louis, J.M. / Hung, J. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ff0.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ff0.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 1ff0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1ff0 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1ff0 | HTTPS FTP |
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-Related structure data
Related structure data | 1fejC 1fffC 1ffiC 1fg6C 1fg8C 1fgcC 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 biological assembly is a dimer consisting of chains C and D |
-Components
#1: Protein | Mass: 10724.654 Da / Num. of mol.: 2 / Mutation: K45I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04587, HIV-1 retropepsin #2: Chemical | ChemComp-2NC / | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 770.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68N11O8 Details: SEQUENCE ANALOGOUS TO THE p2-NC PROCESSING SITE IN HIV-1 References: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR 2NC HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN PLACE OF THE SCISSILE AMIDE. THE ...THE INHIBITOR 2NC HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN PLACE OF THE SCISSILE AMIDE. THE COORDINATE | 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: CITRATE/PHOSPHATE BUFFER 0.05M, DTT 10MM, DMSO 10%, SATURATED AMMONIUM SULPHATE 25-50%, PROTEIN 2-5 MG/ML. pH 5.0-6.5 VAPOR DIFFUSION, HANGING DROP at 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: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.037 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.037 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 1.85→1.93 Å / Rmerge(I) obs: 0.178 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 1.85→8 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 1 / % reflection Rfree: 5.9 % / Rfactor obs: 0.201 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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