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Yorodumi- PDB-2idw: Crystal structure analysis of HIV-1 protease mutant V82A with a p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2idw | |||||||||
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Title | Crystal structure analysis of HIV-1 protease mutant V82A with a potent non-peptide inhibitor (UIC-94017) | |||||||||
Components | Protease | |||||||||
Keywords | HYDROLASE / HIV-1 PROTEASE / MUTANT / DIMER / INHIBITOR / UIC-94017 | |||||||||
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 / identical protein binding Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Manna, D. / Hussain, A.K. / Leshchenko, S. / Ghosh, A.K. / Louis, J.M. / Harrison, R.W. / Weber, I.T. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: High Resolution Crystal Structures of HIV-1 Protease with a Potent Non-Peptide Inhibitor (Uic-94017) Active Against Multi-Drug-Resistant Clinical Strains. Authors: Tie, Y. / Boross, P.I. / Wang, Y.F. / Gaddis, L. / Hussain, A.K. / Leshchenko, S. / Ghosh, A.K. / 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 | 2idw.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2idw.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 2idw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/2idw ftp://data.pdbj.org/pub/pdb/validation_reports/id/2idw | HTTPS FTP |
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-Related structure data
Related structure data | 2ienC 2ieoC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10712.623 Da / Num. of mol.: 2 / Fragment: residues 500-598 Mutation: Q7K, L33I, L63I, C67A, V82A, C95A, Q107K, L133I, L163I, C167A, V182A, C195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: gag, pol / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P03368, UniProt: Q7SSI0*PLUS, HIV-1 retropepsin |
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-Non-polymers , 7 types, 271 molecules
#2: Chemical | ChemComp-CL / | ||||||||||
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#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-ACY / #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-017 / ( | #8: 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: 2.07 Å3/Da / Density % sol: 40.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: AMMONIUM SULFATE, CITRIC PHOSPHATE, DMSO, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 74707 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.196 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAZ Resolution: 1.1→10 Å / Num. parameters: 25871 / Num. restraintsaints: 24400 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 43 / Occupancy sum hydrogen: 1624 / Occupancy sum non hydrogen: 1768 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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