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Yorodumi- PDB-1ebk: Structural and kinetic analysis of drug resistant mutants of HIV-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ebk | ||||||
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Title | Structural and kinetic analysis of drug resistant mutants of HIV-1 protease | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.06 Å | ||||||
Authors | Mahalingam, B. / Louis, J.M. / Reed, C.C. / Adomat, J.M. / Krouse, J. / Wang, Y.F. / Harrison, R.W. / Weber, I.T. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1999 Title: Structural and kinetic analysis of drug resistant mutants of HIV-1 protease. Authors: Mahalingam, B. / Louis, J.M. / Reed, C.C. / Adomat, J.M. / Krouse, J. / Wang, Y.F. / 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 | 1ebk.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ebk.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ebk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1ebk ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1ebk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a dimer consisting of chains C and D or chains E and F |
-Components
#1: Protein | Mass: 10711.611 Da / Num. of mol.: 4 / Fragment: FRAGMENT 69-167 / Mutation: Q7K, R8Q, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATIONS Q7K, R8Q, L33I, L63I, C67A, C95A STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, WHILE RETAINING ACTIVITY SIMILAR TO WILD-TYPE HIV-1 PROTEASE Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin #2: Chemical | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H70N11O8 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 | PEPTIDE INHIBITOR 0Q4 HAS A REDUCED PEPTIDE (-CH2-NH) INSTEAD OF THE NORMAL PEPTIDE LINK (-CO-NH). | Sequence details | ENGINEERED MUTATIONS Q7K, R8Q, L33I, L63I, C67A, C95A STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, ...ENGINEERED | |
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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: 2.14 Å3/Da / Density % sol: 42.58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: CITRATE/PHOSPHATE BUFFER 0.05M, DTT 10MM, DMSO 10%, SATURATED AMMONIUM SULPHATE (25-50%), PROTEIN 2-5 MG/ML, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / PH range low: 5.2 / PH range high: 4.7 | ||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Num. obs: 19007 / % possible obs: 79.2 % / Rmerge(I) obs: 0.084 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.06→8 Å / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 2.06→8 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.55 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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