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- PDB-1bdq: HIV-1 (2:31-37, 47, 82) PROTEASE COMPLEXED WITH INHIBITOR SB203386 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bdq | ||||||
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Title | HIV-1 (2:31-37, 47, 82) PROTEASE COMPLEXED WITH INHIBITOR SB203386 | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | HYDROLASE / AIDS / POLYPROTEIN / ASPARTYL PROTEASE / ACID PROTEASE / HYDROXYETHYLENE ISOSTERE INHIBITOR / SUBSTRATE ANALOGUE INHIBITOR | ||||||
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 | ![]() | ||||||
![]() | Swairjo, M.A. / Abdel-Meguid, S.S. | ||||||
![]() | ![]() Title: Structural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease. Authors: Swairjo, M.A. / Towler, E.M. / Debouck, C. / Abdel-Meguid, S.S. #1: ![]() Title: Identification of a Loop Outside the Active Site Cavity of the Human Immunodeficiency Virus Proteases which Confers Inhibitor Specificity Authors: Towler, E.M. / Thompson, S.K. / Tomaszek, T. / Debouck, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.8 KB | Display | ![]() |
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PDB format | ![]() | 34.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.9 KB | Display | ![]() |
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Full document | ![]() | 738.7 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bdlC ![]() 1bdrC ![]() 1sbgS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 10683.630 Da / Num. of mol.: 2 Mutation: T31S, V32I, L33V, E34A, E35G, M36I, S37E, I47V, V82I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-IM1 / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: HANGING DROP VAPOUR DIFFUSION, BY MIXING EQUAL VOLUMES OF RESERVOIR AND SAMPLE, 21 DEGREES C. RESERVOIR: 35% 3.5 MG/ML PROTEIN/INHIBITOR COMPLEX AT 1:5 MOLAR RATIO., pH 5.6, vapor diffusion - ...Details: HANGING DROP VAPOUR DIFFUSION, BY MIXING EQUAL VOLUMES OF RESERVOIR AND SAMPLE, 21 DEGREES C. RESERVOIR: 35% 3.5 MG/ML PROTEIN/INHIBITOR COMPLEX AT 1:5 MOLAR RATIO., pH 5.6, vapor diffusion - hanging drop, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 5858 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 6.4 / Rsym value: 0.08 / % possible all: 53.7 |
Reflection | *PLUS Num. measured all: 43218 |
Reflection shell | *PLUS % possible obs: 53.7 % |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1SBG Resolution: 2.5→20 Å / Rfactor Rfree error: 0.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 19.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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