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Yorodumi- PDB-2zga: HIV-1 protease in complex with a dimethylallyl decorated pyrrolid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zga | ||||||
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Title | HIV-1 protease in complex with a dimethylallyl decorated pyrrolidine based inhibitor (hexagonal space group) | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.65 Å | ||||||
Authors | Boettcher, J. / Blum, A. / Heine, A. / Diederich, W.E. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Two Solutions for the Same Problem: Multiple Binding Modes of Pyrrolidine-Based HIV-1 Protease Inhibitors Authors: Blum, A. / Bottcher, J. / Dorr, S. / Heine, A. / Klebe, G. / Diederich, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zga.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zga.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/2zga ftp://data.pdbj.org/pub/pdb/validation_reports/zg/2zga | HTTPS FTP |
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-Related structure data
Related structure data | 3cktC 2pqzS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Plasmid: peT11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(D3)pLysS / References: UniProt: P03367, HIV-1 retropepsin |
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#2: Chemical | ChemComp-YDP / ( |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE HALF PART OF YDP EXISTS IN THE DIMER WHICH IS GENERATED BY SYMMETRY OPERATION, 7_555. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 3M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 196 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 29, 2007 Details: double crystal monochromator with two sets of mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25 Å / Num. all: 11774 / Num. obs: 11774 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4.3 / Num. unique all: 559 / Rsym value: 0.386 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: 2PQZ(monomer) Resolution: 1.65→10 Å / Num. parameters: 3215 / Num. restraintsaints: 3078 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 778 / Occupancy sum non hydrogen: 798 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→10 Å
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Refine LS restraints |
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