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- PDB-1gnm: HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASP (V82D) COMPLEXE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gnm | ||||||
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Title | HIV-1 PROTEASE MUTANT WITH VAL 82 REPLACED BY ASP (V82D) COMPLEXED WITH U89360E (INHIBITOR) | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | HYDROLASE (ACID PROTEASE) / ASPARTIC PROTEASE / HIV / MUTANT / INHIBITOR / U-89360E | ||||||
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 | ![]() | ||||||
![]() | Hong, L. / Treharne, A. / Hartsuck, J.A. / Foundling, S. / Tang, J. | ||||||
![]() | ![]() Title: Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases. Authors: Hong, L. / Treharne, A. / Hartsuck, J.A. / Foundling, S. / Tang, J. #1: ![]() Title: Effect of Point Mutations on the Kinetics and the Inhibition of Human Immunodeficiency Virus Type 1 Protease: Relationship to Drug Resistance Authors: Lin, Y. / Lin, X. / Hong, L. / Foundling, S. / Heinrikson, R.L. / Thaisrivongs, S. / Leelamanit, W. / Raterman, D. / Shah, M. / Dunn, B.M. / al., et | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495 KB | Display | ![]() |
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Full document | ![]() | 512.7 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 12 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.49763, -0.86739, 0.00201), Vector: |
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Components
#1: Protein | Mass: 10819.712 Da / Num. of mol.: 2 / Mutation: V82D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P03368, UniProt: P03366*PLUS, RNA-directed DNA polymerase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THERE ARE TWO ORIENTATIO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.82 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / % possible obs: 92.5 % / Rmerge(I) obs: 0.044 |
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Processing
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Refinement | Resolution: 2.3→8 Å / σ(F): 3 /
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Displacement parameters | Biso mean: 18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.175 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |