[English] 日本語
Yorodumi- PDB-3vf7: Crystal Structure of HIV-1 Protease Mutant L76V with novel P1'-Li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vf7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of HIV-1 Protease Mutant L76V with novel P1'-Ligands GRL-02031 | ||||||
Components | protease | ||||||
Keywords | hydrolase/hydrolase inhibitor / protease inhibitor / P1'-ligand / 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 / 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 / host cell plasma membrane / virion membrane / structural molecule activity / 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: 1.3 Å | ||||||
Authors | Yu, X.X. / Wang, Y.F. / Chang, Y.C.E. / Weber, I.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring. Authors: Chang, Y.C. / Yu, X. / Zhang, Y. / Tie, Y. / Wang, Y.F. / Yashchuk, S. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vf7.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vf7.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vf7 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vf7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3vf5C 3vfaC 3vfbC 2ienS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10726.650 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q507K, L533I, L563I, C567A, L576V, C595A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE) Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P03367, HIV-1 retropepsin |
---|
-Non-polymers , 5 types, 201 molecules
#2: Chemical | ChemComp-031 / ( | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 53.99 % |
---|---|
Crystal grow | Temperature: 298 K Details: 0.9 - 1.2 M NaCl/NaOAc buffer at pH=4.2-5.4. The ratio for protein/inhibitor is 1:5, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 4.2-5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2009 |
Radiation | Monochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 56338 / % possible obs: 98.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.1 / % possible all: 86.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IEN Resolution: 1.3→10 Å / Num. parameters: 17044 / Num. restraintsaints: 22325 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 21 / Occupancy sum hydrogen: 1649.75 / Occupancy sum non hydrogen: 1726 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|