- PDB-7d83: Crystal structure of HIV-1 integrase catalytic core domain in com... -
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Basic information
Entry
Database: PDB / ID: 7d83
Title
Crystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-(2-(3-cyclohexylureido)-3,6-dimethyl-5-(5-methylchroman-6-yl)pyridin-4-yl)acetic acid
Components
Integrase
Keywords
VIRAL PROTEIN / HIV-1 Integrase
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
Mass: 18434.723 Da / Num. of mol.: 1 / Mutation: F1332K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5) Strain: isolate NY5 / Production host: Escherichia coli (E. coli) References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Resolution: 2.43→62.62 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.896 / SU B: 17.868 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2779
359
4.6 %
RANDOM
Rwork
0.2239
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-
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obs
0.2263
7444
99.86 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
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