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Yorodumi- PDB-2p8l: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p8l | ||||||
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Title | Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide ELLELDKWASLWN | ||||||
Components |
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Keywords | VIRAL PROTEIN / nmAb 2F5 / HIV-1 / gp41 epitope | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Julien, J.P. / Bryson, S. / Pai, E.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site. Authors: Julien, J.P. / Bryson, S. / Nieva, J.L. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p8l.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p8l.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 2p8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/2p8l ftp://data.pdbj.org/pub/pdb/validation_reports/p8/2p8l | HTTPS FTP |
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-Related structure data
Related structure data | 2p8mC 2p8pC 2pr4C 3d0lC 3d0vC 3droC 3drqC C: citing same article (ref.) |
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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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Details | The biological assembly is the light chain and the heavy chain coming together to form the Fab' fragment that interacts with the peptide |
-Components
#1: Antibody | Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 24985.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#3: Protein/peptide | Mass: 1617.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide |
#4: 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: 3.34 Å3/Da / Density % sol: 63.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M NaCitrate, 20% 2-propanol, 16-20% PEG 4K, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→43.69 Å / Num. obs: 25049 / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.054 |
Reflection shell | Highest resolution: 2.44 Å / Rmerge(I) obs: 0.274 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→43.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 274434.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.5597 Å2 / ksol: 0.365832 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 43 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.44→43.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.59 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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