+Open data
-Basic information
Entry | Database: PDB / ID: 1i5y | ||||||
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Title | HIV-1 GP41 CORE | ||||||
Components | TRANSMEMBRANE GLYCOPROTEIN (GP41) | ||||||
Keywords | VIRAL PROTEIN / GP41 / HIV-1 / MEMBRANE FUSION / HIV-1 INHIBITION | ||||||
Function / homology | Function and homology information host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Liu, J. / Lu, M. | ||||||
Citation | Journal: J.Virol. / Year: 2001 Title: Structural and functional analysis of interhelical interactions in the human immunodeficiency virus type 1 gp41 envelope glycoprotein by alanine-scanning mutagenesis. Authors: Lu, M. / Stoller, M.O. / Wang, S. / Liu, J. / Fagan, M.B. / Nunberg, J.H. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of this protein is not available in any sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i5y.cif.gz | 24.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i5y.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i5y ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i5y | HTTPS FTP |
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-Related structure data
Related structure data | 1i5xC 1sztS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7893.779 Da / Num. of mol.: 1 / Fragment: N34(L6)C28 / Mutation: G572A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q76270 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 4000, sodium acetate, ammonium sulphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 20, 2000 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 23645 / Num. obs: 3507 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 7.3 / Num. unique all: 348 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SZT Resolution: 2.1→35.99 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 935711.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.58 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→35.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
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Xplor file |
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