+Open data
-Basic information
Entry | Database: PDB / ID: 2bpy | ||||||
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Title | HIV-1 protease-inhibitor complex | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / 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 ...symbiont-mediated activation of host apoptosis / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Munshi, S. / Chen, Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Rapid X-ray diffraction analysis of HIV-1 protease-inhibitor complexes: inhibitor exchange in single crystals of the bound enzyme. Authors: Munshi, S. / Chen, Z. / Li, Y. / Olsen, D.B. / Fraley, M.E. / Hungate, R.W. / Kuo, L.C. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Crystal Structure at 1.9-A Resolution of Human Immunodeficiency Virus (HIV) II Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the HIV Proteases Authors: Chen, Z. / Li, Y. / Chen, E. / Hall, D.L. / Darke, P.L. / Culberson, C. / Shafer, J.A. / Kuo, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bpy.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bpy.ent.gz | 38.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bpy ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bpy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THERE IS ONE PROTEASE DIMER IN AN ASYMMETRICAL UNIT. THE TWO MOLECULES ARE LABELED AS CHAIN A AND CHAIN B. THERE IS ONE L-739,622 INHIBITOR MOLECULE LABELED AS 3IN. |
-Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH L-739,622 / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: HIV-1 PROTEASE FROM THE NY5 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P04587, HIV-1 retropepsin #2: Chemical | ChemComp-3IN / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 16008 / % possible obs: 81.8 % / Num. measured all: 95383 / Rmerge(I) obs: 0.048 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.197 / Rfactor obs: 0.197 / Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |