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Yorodumi- PDB-3bva: Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bva | ||||||
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Title | Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor | ||||||
Components | Protease (Retropepsin) | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / DRUG RESISTANCE / HIV-1 / 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 / viral genome integration into host DNA / RNA-directed DNA polymerase ...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-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 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.05 Å | ||||||
Authors | Liu, F. / Weber, I.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Effect of the Active Site D25N Mutation on the Structure, Stability, and Ligand Binding of the Mature HIV-1 Protease. Authors: Sayer, J.M. / Liu, F. / Ishima, R. / Weber, I.T. / Louis, J.M. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor. Authors: Ishima, R. / Torchia, D.A. / Lynch, S.M. / Gronenborn, A.M. / Louis, J.M. #2: Journal: J.Mol.Biol. / Year: 2005 Title: Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S. Authors: Liu, F. / Boross, P.I. / Wang, Y.F. / Tozser, J. / Louis, J.M. / 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 | 3bva.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bva.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bva ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bva | HTTPS FTP |
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-Related structure data
Related structure data | 3bvbC 1dazS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10739.691 Da / Num. of mol.: 2 / Mutation: Q7K, D25N, L33I, L63I, C67A, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: GAG-POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-2NC / | #4: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR 2NC IS A P2/NC ANALOG. IT HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN PLACE OF ...THE INHIBITOR 2NC IS A P2/NC ANALOG. IT HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN PLACE OF THE SCISSILE AMIDE | |
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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: 2.63 Å3/Da / Density % sol: 54.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 10% SODIUM CHLORIDE, CITRATE-PHOSPHATE BUFFER, 7-8% DMSO, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2000 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. all: 102685 / Num. obs: 97551 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.05→1.09 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB entry 1DAZ Resolution: 1.05→10 Å / Num. parameters: 17901 / Num. restraintsaints: 23143 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 37 / Occupancy sum hydrogen: 1663.41 / Occupancy sum non hydrogen: 1775.83 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→10 Å
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Refine LS restraints |
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