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Yorodumi- PDB-4upj: HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE MUTANT WITH LYS 57 R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4upj | ||||||
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Title | HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE MUTANT WITH LYS 57 REPLACED BY LEU (K57L) COMPLEX WITH U097410 [4-HYDROXY-3-[1-[3-[[[[(TERT-BUTYLOXYCARBONYL) AMINOMETHYL]CARBONYL]AMINO]PHENYL]PROPYL]COUMARIN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4upj.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4upj.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 4upj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4upj_validation.pdf.gz | 455.8 KB | Display | wwPDB validaton report |
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Full document | 4upj_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 4upj_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 4upj_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upj ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upj | HTTPS FTP |
-Related 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: 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-U04 / ({ | #3: Water | ChemComp-HOH / | Nonpolymer details | REGARDING RESIDUE U04 [THE INHIBITOR]: ATOMS OA2 AND OA3 ARE, RESPECTIVELY, THE CARBONYL OXYGEN AND ...REGARDING RESIDUE U04 [THE INHIBITOR]: ATOMS OA2 AND OA3 ARE, RESPECTIVE | |
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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: 2.18 Å3/Da / Density % sol: 43.67 % | ||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 24, 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: 1.9→10 Å / Num. obs: 12378 / % possible obs: 78.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.1 / % possible all: 56.6 |
Reflection | *PLUS Num. obs: 12488 / % possible obs: 80 % / Num. measured all: 55194 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EARLIER STRUCTURE Resolution: 1.9→10 Å / σ(F): 2 Details: THERE IS NO ELECTRON DENSITY BEYOND CB OF RESIDUE GLU 37.
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CEDAR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |