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- PDB-3k4v: New crystal form of HIV-1 Protease/Saquinavir structure reveals c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k4v | ||||||
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Title | New crystal form of HIV-1 Protease/Saquinavir structure reveals carbamylation of N-terminal proline | ||||||
![]() | (HIV-1 Protease) x 2 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / CARBAMYLATION / AIDS / Aspartyl protease / Capsid maturation / Capsid protein | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Olajuyigbe, F.M. / Demitri, N. / Ajele, J.O. / Maurizio, E. / Randaccio, L. / Geremia, S. | ||||||
![]() | ![]() Title: Carbamylation of N-terminal proline. Authors: Olajuyigbe, F.M. / Demitri, N. / Ajele, J.O. / Maurizio, E. / Randaccio, L. / Geremia, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.4 KB | Display | ![]() |
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PDB format | ![]() | 149.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a1eS S: Starting model for refinement |
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Similar 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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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 10767.702 Da / Num. of mol.: 2 / Mutation: Q7K L33I L63I C67A C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K L33I L63I C67A C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 196 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/ROC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ROC.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-DMS / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE INHIBITOR ROC IS A HYDROXYETHSequence details | CARBAMYLAT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE, DMSO, SODIUM CITRATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2008 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→14.71 Å / Num. all: 209382 / Num. obs: 72637 / % possible obs: 97.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.39→1.47 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2 / % possible all: 80.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2A1E Resolution: 1.39→10 Å / Num. parameters: 31932 / Num. restraintsaints: 42256 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 29 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3332.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→10 Å
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Refine LS restraints |
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