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Yorodumi- PDB-3mlv: Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with an NO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mlv | ||||||
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Title | Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with an NOF V3 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction | ||||||
Function / homology | Function and homology information host cell endosome membrane / membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Kong, X.-P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Conserved structural elements in the V3 crown of HIV-1 gp120. Authors: Jiang, X. / Burke, V. / Totrov, M. / Williams, C. / Cardozo, T. / Gorny, M.K. / Zolla-Pazner, S. / Kong, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mlv.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mlv.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mlv_validation.pdf.gz | 461.9 KB | Display | wwPDB validaton report |
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Full document | 3mlv_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 3mlv_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 3mlv_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mlv ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mlv | HTTPS FTP |
-Related structure data
Related structure data | 3go1C 3mlrC 3mlsC 3mltC 3mluC 3mlwC 3mlxC 3mlyC 3mlzC 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23357.996 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #2: Antibody | Mass: 24191.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #3: Protein/peptide | Mass: 2220.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / References: UniProt: Q79790 #4: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE FABS WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FABS WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ARE UNKNOWN. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.63 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 3350, 0.2 M MgCl2, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2007 Details: a KOHZU double crystal monochromator with a sagittally focused second crystal. Two spherical mirrors, one will be rhodium coated. User choice of either mirror depending on the desired energy | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.48→50 Å / Num. obs: 25853 / % possible obs: 90.6 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.5 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→35.54 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.39 / σ(F): 1.96 / Phase error: 47.07 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.651 Å2 / ksol: 0.309 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.48→35.54 Å
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Refine LS restraints |
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LS refinement shell |
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