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Yorodumi- PDB-1g35: CRYSTAL STRUCTURE OF HIV-1 PROTEASE IN COMPLEX WITH INHIBITOR, AHA024 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g35 | ||||||
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Title | CRYSTAL STRUCTURE OF HIV-1 PROTEASE IN COMPLEX WITH INHIBITOR, AHA024 | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE / Protein-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 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lindberg, J. / Unge, T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2001 Title: Synthesis and comparative molecular field analysis (CoMFA) of symmetric and nonsymmetric cyclic sulfamide HIV-1 protease inhibitors. Authors: Schaal, W. / Karlsson, A. / Ahlsen, G. / Lindberg, J. / Andersson, H.O. / Danielson, U.H. / Classon, B. / Unge, T. / Samuelsson, B. / Hulten, J. / Hallberg, A. / Karlen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g35.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g35.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 1g35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g35 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g35 | HTTPS FTP |
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-Related structure data
Related structure data | 1g2kC 1ajxS 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
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH7 / Production host: Escherichia coli (E. coli) References: UniProt: P03368, UniProt: P03366*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-AHF / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 mM MES, 0.4 M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.375 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 3, 1998 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 22833 / Num. obs: 19437 / % possible obs: 85.1 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.8→25 Å / Redundancy: 1.16 % / Rmerge(I) obs: 0.31 / Num. unique all: 1795 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ajx Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→50 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 0 % / Rfactor Rfree: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 85 % / Rfactor obs: 0.1949 |