+Open data
-Basic information
Entry | Database: PDB / ID: 6upj | ||||||
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Title | HIV-2 PROTEASE/U99294 COMPLEX | ||||||
Components | HIV-2 PROTEASE | ||||||
Keywords | HYDROLASE / ACID PROTEASE / HIV-2 PROTEASE-INHIBITOR COMPLEX / PROTEIN-SUBSTRATE INTERACTION / ASPARTYL PROTEASE | ||||||
Function / homology | Function and homology information HIV-2 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-2 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 | Human immunodeficiency virus 2 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Watenpaugh, K.D. / Mulichak, A.M. / Finzel, B.C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1995 Title: Use of medium-sized cycloalkyl rings to enhance secondary binding: discovery of a new class of human immunodeficiency virus (HIV) protease inhibitors. Authors: Romines, K.R. / Watenpaugh, K.D. / Tomich, P.K. / Howe, W.J. / Morris, J.K. / Lovasz, K.D. / Mulichak, A.M. / Finzel, B.C. / Lynn, J.C. / Horng, M.-M. / Schwende, F.J. / Ruwart, M.J. / Zipp, ...Authors: Romines, K.R. / Watenpaugh, K.D. / Tomich, P.K. / Howe, W.J. / Morris, J.K. / Lovasz, K.D. / Mulichak, A.M. / Finzel, B.C. / Lynn, J.C. / Horng, M.-M. / Schwende, F.J. / Ruwart, M.J. / Zipp, G.L. / Chong, K.-T. / Dolak, L.A. / Toth, L.N. / Howard, G.M. / Rush, B.D. / Wilkinson, K.F. / Possert, P.L. / Dalga, R.J. / Hinshaw, R.R. #1: Journal: J.Med.Chem. / Year: 1995 Title: Structure-based design of sulfonamide-substituted non-peptidic HIV protease inhibitors. Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.-T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / Mcgrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.R. / ...Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.-T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / Mcgrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.R. / Zipp, G.L. / Ruwart, M.J. / Schwende, F.J. / Zhong, W.-Z. / Padbury, G.E. / Dalga, R.J. / Shiou, L. / Possert, P.L. / Rush, B.D. / Wilkinson, K.F. / Howard, G.M. / Toth, L.N. / Williams, M.G. / Kakuk, T.J. / Cole, S.L. / Zaya, R.M. / Lovasz, K.D. / Morris, J.K. / Romines, K.R. / Thaisrivongs, S. / Aristoff, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6upj.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6upj.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 6upj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6upj_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 6upj_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 6upj_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 6upj_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/6upj ftp://data.pdbj.org/pub/pdb/validation_reports/up/6upj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10712.315 Da / Num. of mol.: 2 / Mutation: K57L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04584, HIV-1 retropepsin #2: Chemical | ChemComp-NIU / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.37 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 4-7 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN AT 8-10 MG/L AND WELL SOLUTION OF 30-35%(W/V) PEG 4000 IN 0.1 M HEPES AND PH RANGE 6.8 - 7.6., pH ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 4-7 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN AT 8-10 MG/L AND WELL SOLUTION OF 30-35%(W/V) PEG 4000 IN 0.1 M HEPES AND PH RANGE 6.8 - 7.6., pH 7.0, vapor diffusion - hanging drop PH range: 6.8-7.6 | |||||||||||||||||||||||||
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: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Mar 9, 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: 2.34→10 Å / Num. obs: 7557 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.34→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 4.37 / % possible all: 38 |
Reflection | *PLUS Num. measured all: 27701 |
Reflection shell | *PLUS % possible obs: 38 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EARLIER STRUCTURE FROM SAME LABORATORY Resolution: 2.34→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.34→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CEDAR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |