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- PDB-3is9: Crystal structure of the HIV-1 reverse transcriptase (RT) in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3is9 | ||||||
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Title | Crystal structure of the HIV-1 reverse transcriptase (RT) in complex with the alkenyldiarylmethane (ADAM) Non-nucleoside RT Inhibitor dimethyl 3,3'-(6-methoxy-6-oxohex-1-ene-1,1-diyl)bis(5-cyano-6-methoxybenzoate). | ||||||
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![]() | transferase/hydrolase / NNRTI / NONNUCLEOSIDE INHIBITOR / AIDS / HIV / P51/P66 / ADAM / Aspartyl protease / Cell membrane / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Hydrolase / Lipoprotein / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / RNA-binding / RNA-directed DNA polymerase / Transferase / Viral nucleoprotein / Virion / Zinc / Zinc-finger / transferase-hydrolase 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 | ![]() ![]() ![]() | ||||||
![]() | Ho, W.C. / Bauman, J.D. / Das, K. / Arnold, E. | ||||||
![]() | ![]() Title: Crystallographic study of a novel subnanomolar inhibitor provides insight on the binding interactions of alkenyldiarylmethanes with human immunodeficiency virus-1 reverse transcriptase. Authors: Cullen, M.D. / Ho, W.C. / Bauman, J.D. / Das, K. / Arnold, E. / Hartman, T.L. / Watson, K.M. / Buckheit, R.W. / Pannecouque, C. / De Clercq, E. / Cushman, 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 | ![]() | 212.6 KB | Display | ![]() |
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PDB format | ![]() | 167.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 864.2 KB | Display | ![]() |
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Full document | ![]() | 915.6 KB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3irxC ![]() 2zd1S C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 64046.293 Da / Num. of mol.: 1 / Mutation: C879S, K771A, K772A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Production host: ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Production host: ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase |
#3: Chemical | ChemComp-AC7 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 277 K / pH: 6.4 Details: 11% PEG8000, 15 mM MgSO4, 10 mM Spermine, 100 mM Ammonium sulphate, 50 mM imidazole pH 6.4., temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→40 Å / Num. all: 41647 / Num. obs: 41074 / % possible obs: 98.6 % / Redundancy: 11.67 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.3 |
Reflection shell | Highest resolution: 2.55 Å / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZD1 Resolution: 2.55→40 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 80.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→40 Å
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