+Open data
-Basic information
Entry | Database: PDB / ID: 1xl2 | ||||||
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Title | HIV-1 Protease in complex with pyrrolidinmethanamine | ||||||
Components | PROTEASE RETROPEPSIN | ||||||
Keywords | HYDROLASE / Aspartyl Protease / HIV Protease / Pyrrolidine Inhibitor | ||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Boettcher, J. / Specker, E. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2005 Title: An Old Target Revisited: Two New Privileged Skeletons and an Unexpected Binding Mode For HIV-Protease Inhibitors Authors: Specker, E. / Boettcher, J. / Lilie, H. / Heine, A. / Schoop, A. / Muller, G. / Griebenow, N. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xl2.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xl2.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xl2_validation.pdf.gz | 893.9 KB | Display | wwPDB validaton report |
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Full document | 1xl2_full_validation.pdf.gz | 895.5 KB | Display | |
Data in XML | 1xl2_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1xl2_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/1xl2 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/1xl2 | HTTPS FTP |
-Related structure data
Related structure data | 1xl5C 1b6n 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
#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 / Gene: gag-pol / Plasmid: p566 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | #3: Chemical | ChemComp-189 / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 33.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: NaCl, Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 27, 2004 / Details: silicon mirrors, double silicon crystal |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 29849 / Num. obs: 29849 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.063 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.54 / % possible all: 77.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B6N 1b6n Resolution: 1.5→8 Å / Num. parameters: 7111 / Num. restraintsaints: 6506 / Cross valid method: FREE R / σ(F): 0 / 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: 5 / Occupancy sum hydrogen: 1604 / Occupancy sum non hydrogen: 1755 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→8 Å
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Refine LS restraints |
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