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Yorodumi- PDB-3k4v: New crystal form of HIV-1 Protease/Saquinavir structure reveals c... -
+Open data
-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 | ||||||
Components | (HIV-1 Protease) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / CARBAMYLATION / AIDS / Aspartyl protease / Capsid maturation / Capsid protein | ||||||
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 / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Olajuyigbe, F.M. / Demitri, N. / Ajele, J.O. / Maurizio, E. / Randaccio, L. / Geremia, S. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k4v.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k4v.ent.gz | 149.5 KB | Display | PDB format |
PDBx/mmJSON format | 3k4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k4v ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k4v | HTTPS FTP |
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-Related structure data
Related structure data | 2a1eS S: Starting model for refinement |
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Similar 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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-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.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin #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.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin |
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-Non-polymers , 4 types, 196 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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