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- PDB-3mlw: Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mlw | ||||||
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Title | Crystal structure of anti-HIV-1 V3 Fab 1006-15D in complex with an MN V3 peptide | ||||||
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![]() | IMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kong, X.-P. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.3 KB | Display | ![]() |
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PDB format | ![]() | 150.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3go1C ![]() 3mlrC ![]() 3mlsC ![]() 3mltC ![]() 3mluC ![]() 3mlvC ![]() 3mlxC ![]() 3mlyC ![]() 3mlzC C: citing same article ( |
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Similar structure data |
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Links
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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: 23035.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Antibody | Mass: 24574.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein/peptide | Mass: 2711.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ...AUTHORS STATE THAT THE FAB WERE MADE BY ENZYME DIGESTION, THEREFORE THE REAL ENDINGS OF THE CHAINS ARE UNKNOWN. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.71 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, K dihydrogen phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 2007 Details: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 29061 / % possible obs: 94 % / Rmerge(I) obs: 0.156 / Χ2: 0.825 / Net I/σ(I): 5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.98 Å2 / Biso mean: 48.043 Å2 / Biso min: 9.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→42.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.771 Å / Total num. of bins used: 20
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