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- PDB-3bxs: Crystal Structures Of Highly Constrained Substrate And Hydrolysis... -
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Basic information
Entry | Database: PDB / ID: 3bxs | ||||||
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Title | Crystal Structures Of Highly Constrained Substrate And Hydrolysis Products Bound To HIV-1 Protease. Implications For Catalytic Mechanism | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE / HIV protease / HIVPR / substrate / product / AIDS / Aspartyl protease / Capsid maturation / Core protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc / Zinc-finger | ||||||
Function / homology | ![]() 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 | ||||||
Method | ![]() ![]() | ||||||
![]() | Tyndall, J.D. / Pattenden, L.K. / Reid, R.C. / Hu, S.H. / Alewood, D. / Alewood, P.F. / Walsh, T. / Fairlie, D.P. / Martin, J.L. | ||||||
![]() | ![]() Title: Crystal Structures of Highly Constrained Substrate and Hydrolysis Products Bound to HIV-1 Protease. Implications for the Catalytic Mechanism Authors: Tyndall, J.D. / Pattenden, L.K. / Reid, R.C. / Hu, S.H. / Alewood, D. / Alewood, P.F. / Walsh, T. / Fairlie, D.P. / Martin, J.L. #1: ![]() Title: Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease Authors: Martin, J.L. / Begun, J. / Schindeler, A. / Wickramasinghe, W.A. / Alewood, D. / Alewood, P.F. / Bergman, D.A. / Brinkworth, R.I. / Abbenante, G. / March, D.R. / Reid, R.C. / Fairlie, D.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 59.8 KB | Display | ![]() |
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PDB format | ![]() | 42.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bxrC ![]() 1cpiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10765.687 Da / Num. of mol.: 2 / Fragment: UNP residues 491-589 Mutation: Q7K, L33I, C67(ABA), C95(ABA), Q107K, L133I, C167(ABA), C195(ABA) Source method: obtained synthetically Details: Chemically synthesized protein corresponding to the protease from the HIV1 References: UniProt: P03369, HIV-1 retropepsin #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Acetate, (NH4)2SO4, pH5.5, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 16, 1998 / Details: Yale mirrors |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 22094 / Num. obs: 22094 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.031 / Χ2: 1.056 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1253 / Χ2: 1.084 / % possible all: 52.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CPI Resolution: 1.6→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 73.119 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.933 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.61 Å /
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Xplor file |
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