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- PDB-3qin: Crystal Structure of HIV-1 RNase H p15 with engineered E. coli lo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qin | ||||||
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Title | Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol carboxylic acid inhibitor | ||||||
![]() | Fusion protein of HIV-1 RNase H p15 with engineered E. coli loop | ||||||
![]() | TRANSFERASE / HYDROLASE/INHIBITOR / RNase H / HIV-1 / inhibitor / nuclease / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() DNA replication, removal of RNA primer / integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs ...DNA replication, removal of RNA primer / integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / ribonuclease H / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / DNA recombination / nucleic acid binding / 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 / magnesium ion binding / DNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lansdon, E.B. / Kirschberg, T.A. | ||||||
![]() | ![]() Title: Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors. Authors: Lansdon, E.B. / Liu, Q. / Leavitt, S.A. / Balakrishnan, M. / Perry, J.K. / Lancaster-Moyer, C. / Kutty, N. / Liu, X. / Squires, N.H. / Watkins, W.J. / Kirschberg, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.7 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.8 KB | Display | ![]() |
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Full document | ![]() | 790.5 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qioC ![]() 3qipC ![]() 1hrhS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 16921.463 Da / Num. of mol.: 1 / Fragment: HIV-1 RNase H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Strain: isolate HXB2, K12 / Gene: gag-pol, rnhA, dasF, herA, rnh, sdrA, b0214, JW0204 / Plasmid: pET 30B / Production host: ![]() ![]() References: UniProt: P04585, UniProt: P0A7Y4, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring ...References: UniProt: P04585, UniProt: P0A7Y4, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds, ribonuclease H | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-P1Y / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8M (NH4)2SO4, 100mM HEPES pH 7.5, and 3% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6967→50 Å / Num. obs: 21540 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.6967→1.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HRH Resolution: 1.6967→23.118 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.56 / 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 / Bsol: 59.68 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6967→23.118 Å
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Refine LS restraints |
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LS refinement shell |
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