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Open data
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Basic information
Entry | Database: PDB / ID: 1ody | ||||||
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Title | HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR LP-130 | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | ASPARTIC PROTEASE / RETROPEPSIN / RETROVIRUS / HIV / AIDS | ||||||
Function / homology | ![]() integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / virion membrane / structural molecule activity / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Kervinen, J. / Lubkowski, J. / Zdanov, A. / Wlodawer, A. / Gustchina, A. | ||||||
![]() | ![]() Title: Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV. Authors: Kervinen, J. / Lubkowski, J. / Zdanov, A. / Bhatt, D. / Dunn, B.M. / Hui, K.Y. / Powell, D.J. / Kay, J. / Wlodawer, A. / Gustchina, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.3 KB | Display | ![]() |
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PDB format | ![]() | 39.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 754.3 KB | Display | ![]() |
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Full document | ![]() | 766.4 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fmbC ![]() 4fivC ![]() 1odxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10703.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: PIR: S63716, UniProt: P04585*PLUS, HIV-1 retropepsin #2: Chemical | ChemComp-LP1 / | #3: Water | ChemComp-HOH / | Nonpolymer details | LP-130 (HET ID LP1): ACE-NAL-VAL-STA-ABU-NAL-NH2 WHERE NAL IS NAPHTHYLALANINE, STA IS STATINE, AND ...LP-130 (HET ID LP1): ACE-NAL-VAL-STA-ABU-NAL-NH2 WHERE NAL IS NAPHTHYLAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.62 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 11, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 12082 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.429 / % possible all: 85.1 |
Reflection shell | *PLUS % possible obs: 85.1 % |
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Processing
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: PDB ENTRY 1ODX Resolution: 2→8 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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