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- PDB-3nxn: X-ray structure of ester chemical analogue 'covalent dimer' [Ile5... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nxn | |||||||||
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Title | X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with KVS-1 inhibitor | |||||||||
![]() | protease covalent dimer | |||||||||
![]() | hydrolase/hydrolase inhibitor / beta-barrel / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | ![]() HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Torbeev, V.Y. / Kent, S.B.H. | |||||||||
![]() | ![]() Title: Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Authors: Torbeev, V.Y. / Raghuraman, H. / Hamelberg, D. / Tonelli, M. / Westler, W.M. / Perozo, E. / Kent, S.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.8 KB | Display | ![]() |
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PDB format | ![]() | 42 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fsmC ![]() 3hauC ![]() 3hawC ![]() 3hboC ![]() 3hdkC ![]() 3hloC ![]() 3iawC ![]() 3ka2C ![]() 3nwqC ![]() 3nwxC ![]() 3nxeC ![]() 3nygC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 21892.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical protein synthesis / References: UniProt: P03369*PLUS, HIV-1 retropepsin | ||
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#2: Chemical | ChemComp-KVS / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Citrate, 0.2 M Sodium Phosphate, 30% (w/v) Ammonium Sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2007 |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 17520 / % possible obs: 99.7 % / Observed criterion σ(F): 102.9 / Observed criterion σ(I): 102.9 / Redundancy: 5.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.51 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.292 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.803→1.85 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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