+Open data
-Basic information
Entry | Database: PDB / ID: 7mac | ||||||
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Title | HIV-1 Protease (I84V) in Complex with PD4 (LR4-23) | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / DRUG RESISTANCE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Lockbaum, G.J. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: HIV-1 Protease (I84V) in Complex with PD4 (LR4-23) Authors: Lockbaum, G.J. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mac.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mac.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 7mac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mac_validation.pdf.gz | 752.8 KB | Display | wwPDB validaton report |
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Full document | 7mac_full_validation.pdf.gz | 757.7 KB | Display | |
Data in XML | 7mac_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 7mac_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/7mac ftp://data.pdbj.org/pub/pdb/validation_reports/ma/7mac | HTTPS FTP |
-Related structure data
Related structure data | 6dgxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10817.807 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-XUM / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.16 Å3/Da / Density % sol: 43.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 23-24% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.56 Å / Num. obs: 21270 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.64 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.72 / Num. unique obs: 2021 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6dgx Resolution: 1.7→39.56 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.1 Å2 / Biso mean: 31.0336 Å2 / Biso min: 13.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→39.56 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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