+Open data
-Basic information
Entry | Database: PDB / ID: 1d4j | ||||||
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Title | HIV-1 protease in complex with the inhibitor MSL370 | ||||||
Components | HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE / DIMER | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å | ||||||
Authors | Unge, T. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d4j.cif.gz | 53.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d4j.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 1d4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/1d4j ftp://data.pdbj.org/pub/pdb/validation_reports/d4/1d4j | HTTPS FTP |
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-Related structure data
Related structure data | 1d4hC 1d4iC 1ebwC 1ebyC 1ebzC 1ec1C 1ec2C 1ec3C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer. |
-Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus / Genus: Lentivirus / Strain: BH10 / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin #2: Chemical | ChemComp-MSC / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.12 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 17, 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→14.99 Å / Num. all: 21767 / Num. obs: 21687 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.81→1.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.247 / Num. unique all: 3240 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 92684 / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS Lowest resolution: 1.87 Å |
-Processing
Software |
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Refinement | Resolution: 1.81→14.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1192522.56 / Data cutoff high rms absF: 1192522.56 / 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: 44.41 Å2 / ksol: 0.381 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.92 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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