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Open data
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Basic information
Entry | Database: PDB / ID: 1yth | ||||||
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Title | SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT | ||||||
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![]() | HYDROLASE/PEPTIDE / AIDS / POLYPROTEIN / HYDROLASE / ASPARTYL PROTEASE / ENDONUCLEASE / RNA-DIRECTED DNA POLYMERASE / HYDROLASE-PEPTIDE COMPLEX | ||||||
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 | ![]() ![]() | ||||||
![]() | Rose, R.B. / Craik, C.S. / Douglas, N.L. / Stroud, R.M. | ||||||
![]() | ![]() Title: Three-dimensional structures of HIV-1 and SIV protease product complexes. Authors: Rose, R.B. / Craik, C.S. / Douglas, N.L. / Stroud, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.1 KB | Display | ![]() |
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PDB format | ![]() | 35.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.8 KB | Display | ![]() |
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Full document | ![]() | 425.9 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 12.9 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: (-0.998, -0.055, -0.005), Vector: |
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Components
#1: Protein | Mass: 10801.763 Da / Num. of mol.: 2 / Mutation: CHAIN A, B, Q7K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein/peptide | | Mass: 505.565 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.4 / 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: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Num. obs: 9700 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.08 |
Reflection | *PLUS Highest resolution: 2.2 Å |
Reflection shell | *PLUS % possible obs: 93 % |
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Processing
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Refinement | Resolution: 2.2→7 Å / σ(F): 0
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Displacement parameters | Biso mean: 21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 27 |