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- PDB-3mlt: Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mlt | ||||||
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Title | Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with a UG1033 V3 peptide | ||||||
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![]() | IMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction | ||||||
Function / homology | ![]() | ||||||
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 | ![]() | 335.1 KB | Display | ![]() |
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PDB format | ![]() | 281.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.3 KB | Display | ![]() |
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Full document | ![]() | 543.8 KB | Display | |
Data in XML | ![]() | 65.5 KB | Display | |
Data in CIF | ![]() | 92 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3go1C ![]() 3mlrC ![]() 3mlsC ![]() 3mluC ![]() 3mlvC ![]() 3mlwC ![]() 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23331.873 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Antibody | Mass: 24191.055 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein/peptide | Mass: 2462.764 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: 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: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2 M Na formate, 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: Jun 11, 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: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→50 Å / Num. obs: 62552 / % possible obs: 99.9 % / Rmerge(I) obs: 0.047 / Χ2: 0.335 / Net I/σ(I): 8.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.51 Å2 / Biso mean: 44.123 Å2 / Biso min: 11.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→35.74 Å
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LS refinement shell | Resolution: 2.49→2.555 Å / Total num. of bins used: 20
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