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Yorodumi- PDB-1u8k: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u8k | ||||||
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Title | Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide LELDKWASL | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab complex / HIV-1 Neutralization / gp41 Peptide | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Bryson, S. / Julien, J.-P. / Pai, E.F. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptides and Peptide Mimetics Authors: Bryson, S. / Hynes, R.C. / Cunningham, A. / Dong, A. / Julien, J.-P. / Kunert, R. / Katinger, H. / Klein, M. / 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 | 1u8k.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u8k.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 1u8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/1u8k ftp://data.pdbj.org/pub/pdb/validation_reports/u8/1u8k | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Antibody | Mass: 23391.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#2: Antibody | Mass: 24898.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#3: Protein/peptide | Mass: 1075.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE / Source: (synth.) Human immunodeficiency virus 1 |
#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: 3.02 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: sodium citrate, ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→40 Å / Num. all: 32120 / Num. obs: 28774 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.18 |
Reflection shell | Resolution: 2.24→2.38 Å / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 652470.53 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.4121 Å2 / ksol: 0.398865 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.24→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.24→2.38 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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