[English] 日本語
Yorodumi- PDB-3upj: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE MUTANT WITH LYS 57 R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3upj | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE MUTANT WITH LYS 57 REPLACED BY LEU (K57L) COMPLEX WITH U096333 [4-HYDROXY-3-[1-(PHENYL)PROPYL]-7-METHOXYCOUMARIN] | ||||||
Components | HIV-2 PROTEASE | ||||||
Keywords | HYDROLASE (ACID PROTEASE) | ||||||
Function / homology | Function and homology information HIV-2 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-2 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 2 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Watenpaugh, K.D. / Mulichak, A.M. / Janakiraman, M.N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1995 Title: Structure-based design of novel HIV protease inhibitors: carboxamide-containing 4-hydroxycoumarins and 4-hydroxy-2-pyrones as potent nonpeptidic inhibitors. Authors: Thaisrivongs, S. / Watenpaugh, K.D. / Howe, W.J. / Tomich, P.K. / Dolak, L.A. / Chong, K.-T. / Tomich, C.-S.C. / Tomasselli, A.G. / Turner, S.R. / Strohbach, J.W. / Mulichak, A.M. / ...Authors: Thaisrivongs, S. / Watenpaugh, K.D. / Howe, W.J. / Tomich, P.K. / Dolak, L.A. / Chong, K.-T. / Tomich, C.-S.C. / Tomasselli, A.G. / Turner, S.R. / Strohbach, J.W. / Mulichak, A.M. / Janakiraman, M.N. / Moon, J.B. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.R. / Curry, K.A. / Rothrock, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3upj.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3upj.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 3upj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3upj_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3upj_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 3upj_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 3upj_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/3upj ftp://data.pdbj.org/pub/pdb/validation_reports/up/3upj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10712.315 Da / Num. of mol.: 2 / Mutation: K57L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04584, HIV-1 retropepsin #2: Chemical | ChemComp-U03 / | #3: Water | ChemComp-HOH / | Nonpolymer details | ATOMS OA2 AND OA3 OF RESIDUE U03 [THE INHIBITOR] ARE, RESPECTIVELY, THE CARBONYL OXYGEN AND RING ...ATOMS OA2 AND OA3 OF RESIDUE U03 [THE INHIBITOR] ARE, RESPECTIVE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 23, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 6651 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 2 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.3 / % possible all: 46.7 |
Reflection | *PLUS Num. measured all: 21608 |
Reflection shell | *PLUS % possible obs: 46.7 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: EARLIER STRUCTURE Resolution: 2.5→10 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CEDAR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |