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- PDB-3vfb: Crystal Structure of HIV-1 Protease Mutant N88D with novel P1'-Li... -
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Open data
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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 | ||||||
![]() | protease | ||||||
![]() | hydrolase/hydrolase inhibitor / protease inhibitor / P1'-ligand / hydrolase-hydrolase inhibitor complex | ||||||
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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, X.X. / Wang, Y.F. / Chang, Y.C.E. / Weber, I.T. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.3 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.9 KB | Display | ![]() |
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Full document | ![]() | 780.7 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vf5C ![]() 3vf7C ![]() 3vfaC ![]() 3h5bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: gag-pol / Plasmid: pET11a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 169 molecules ![](data/chem/img/031.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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