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- PDB-2upj: HIV-1 PROTEASE COMPLEX WITH U100313 ([3-[[3-[CYCLOPROPYL [4-HYDRO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2upj | ||||||
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Title | HIV-1 PROTEASE COMPLEX WITH U100313 ([3-[[3-[CYCLOPROPYL [4-HYDROXY-2OXO-6-[1-(PHENYLMETHYL)PROPYL]-2H-PYRAN-3-YL] METHYL]PHENYL]AMINO]-3-OXO-PROPYL]CARBAMIC ACID TERT-BUTYL ESTER) | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | HYDROLASE (ACID PROTEASE) | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Watenpaugh, K.D. / Mulichak, A.M. / Janakiraman, M.N. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.4 KB | Display | ![]() |
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PDB format | ![]() | 36.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455 KB | Display | ![]() |
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Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-U02 / [ | #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR MOLECULE BINDS IN ONE ONE ORIENTATION. HOWEVER, THE CARBOXAMIDE SIDE CHAIN WITH ITS ...THE INHIBITOR MOLECULE BINDS IN ONE ONE ORIENTATIO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % | ||||||||||||||||||
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Crystal grow | pH: 5.2 / Details: pH 5.2 | ||||||||||||||||||
Crystal grow | *PLUS 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: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 5, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→10 Å / Num. obs: 5144 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 30558 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: EARLIER STRUCTURE Resolution: 3→10 Å / σ(F): 2 Details: NO ELECTRON DENSITY WAS OBSERVED BEYOND THE POSITION OF THE BETA-CARBON FOR GLU A 34, ARG A 41, GLN A 61, AND GLN B 18, THE DELTA-CARBON OF LYS A 14, LYS A 43, AND LYS B 55. THEY WERE ...Details: NO ELECTRON DENSITY WAS OBSERVED BEYOND THE POSITION OF THE BETA-CARBON FOR GLU A 34, ARG A 41, GLN A 61, AND GLN B 18, THE DELTA-CARBON OF LYS A 14, LYS A 43, AND LYS B 55. THEY WERE PRESENT DURING REFINEMENT, HOWEVER. IN ADDITION, ATOMS WITH B-FACTORS GREATER THAN 70.0 A**2 MAY BE CONSIDERED TO BE DISORDERED OR NOT SEEN IN THE ELECTRON DENSITY MAPS.
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CEDAR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.164 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |