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Yorodumi- PDB-3vfb: Crystal Structure of HIV-1 Protease Mutant N88D with novel P1'-Li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vfb | ||||||
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Title | Crystal Structure of HIV-1 Protease Mutant N88D 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: 1.55 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vfb.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vfb.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 3vfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vfb ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vfb | HTTPS FTP |
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-Related structure data
Related structure data | 3vf5C 3vf7C 3vfaC 3h5bS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10741.661 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q507K, L533I, L563I, C567A, N588D, 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 |
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-Non-polymers , 5 types, 169 molecules
#2: Chemical | ChemComp-031 / ( | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 298 K / pH: 4.2 Details: NaCl/sodium acetate buffer at pH 4.2 The concentration of protein is no higher than 3 mg/ml. The ratio for protein/inhibitor is 1:5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97181 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 27, 2009 |
Radiation | Monochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97181 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 34554 / % possible obs: 99.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H5B Resolution: 1.55→10 Å / Num. parameters: 16027 / Num. restraintsaints: 20153 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 1635 / Occupancy sum non hydrogen: 1690 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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Refine LS restraints |
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