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- PDB-1ebk: Structural and kinetic analysis of drug resistant mutants of HIV-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ebk | ||||||
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Title | Structural and kinetic analysis of drug resistant mutants of HIV-1 protease | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HIV-1 PROTEASE / HYDROLASE-HYDROLASE INHIBITOR 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Mahalingam, B. / Louis, J.M. / Reed, C.C. / Adomat, J.M. / Krouse, J. / Wang, Y.F. / Harrison, R.W. / Weber, I.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.5 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 528.6 KB | Display | ![]() |
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Full document | ![]() | 549 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 |
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
Software | Name: ![]() | ||||||||||||||||||||||||||||||||||||
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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: ![]() | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.55 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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