+Open data
-Basic information
Entry | Database: PDB / ID: 1iky | ||||||
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Title | HIV-1 Reverse Transcriptase in Complex with the Inhibitor MSC194 | ||||||
Components | (POL POLYPROTEIN) x 2 | ||||||
Keywords | TRANSFERASE / Heterodimer / protein-inhibitor complex | ||||||
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 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Lindberg, J. / Unge, T. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2002 Title: Structural basis for the inhibitory efficacy of efavirenz (DMP-266), MSC194 and PNU142721 towards the HIV-1 RT K103N mutant. Authors: Lindberg, J. / Sigurdsson, S. / Lowgren, S. / Andersson, H.O. / Sahlberg, C. / Noreen, R. / Fridborg, K. / Zhang, H. / Unge, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iky.cif.gz | 207.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iky.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 1iky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/1iky ftp://data.pdbj.org/pub/pdb/validation_reports/ik/1iky | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a heterodimer |
-Components
#1: Protein | Mass: 64500.965 Da / Num. of mol.: 1 / Mutation: K103N, E478Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: BH10 / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 49912.344 Da / Num. of mol.: 1 / Mutation: K1103N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: BH10 / Plasmid: PET11C / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-MSD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.78 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Ammonium Sulphate, Potassium chloride, HEPES, Magnesium Chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 279 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→24.75 Å / Num. all: 32083 / Num. obs: 27395 / % possible obs: 85.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 235.5 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.93→3.08 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.219 / Num. unique all: 1600 / % possible all: 32.3 |
Reflection | *PLUS Num. measured all: 261528 |
Reflection shell | *PLUS % possible obs: 73.6 % / Num. unique obs: 1170 |
-Processing
Software |
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Refinement | Resolution: 3→45.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2848454.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Refined with the CNS program system
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.7476 Å2 / ksol: 0.331188 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→45.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.208 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 57.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.41 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.34 |