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Open data
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Basic information
Entry | Database: PDB / ID: 1d4i | ||||||
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Title | HIV-1 protease in complex with the inhibitor BEA425 | ||||||
![]() | HIV-1 PROTEASE | ||||||
![]() | HYDROLASE / DIMER | ||||||
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 | ![]() ![]() | ||||||
![]() | Unge, T. | ||||||
![]() | ![]() Title: Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors. Authors: Andersson, H.O. / Fridborg, K. / Lowgren, S. / Alterman, M. / Muhlman, A. / Bjorsne, M. / Garg, N. / Kvarnstrom, I. / Schaal, W. / Classon, B. / Danielsson, U.H. / Ahlsen, G. / Nillroth, U. ...Authors: Andersson, H.O. / Fridborg, K. / Lowgren, S. / Alterman, M. / Muhlman, A. / Bjorsne, M. / Garg, N. / Kvarnstrom, I. / Schaal, W. / Classon, B. / Danielsson, U.H. / Ahlsen, G. / Nillroth, U. / Vrang, L. / Oberg, B. / Samuelsson, B. / Hallberg, A. / Unge, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 38.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.1 KB | Display | ![]() |
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Full document | ![]() | 803.8 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1d4hC ![]() 1d4jC ![]() 1ebwC ![]() 1ebyC ![]() 1ebzC ![]() 1ec1C ![]() 1ec2C ![]() 1ec3C 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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Details | The biological assembly is a dimer. |
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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-BEG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.99 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: sodium chloride, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Details: used microseeding | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→27.88 Å / Num. all: 22257 / Num. obs: 21735 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.81→1.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.249 / Num. unique all: 3298 / % possible all: 95.6 |
Reflection | *PLUS Num. measured all: 95666 / Rmerge(I) obs: 0.111 |
Reflection shell | *PLUS Lowest resolution: 1.87 Å |
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Processing
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Refinement | Resolution: 1.81→27.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1251177.33 / Data cutoff high rms absF: 1251177.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: Refined with CNS program system
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.23 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→27.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.92 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 27.9 Å / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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