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Yorodumi- PDB-3mls: Crystal structure of anti-HIV-1 V3 mAb 2557 Fab in complex with a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mls | ||||||
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Title | Crystal structure of anti-HIV-1 V3 mAb 2557 Fab in complex with a HIV-1 gp120 V3 mimotope | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human monoclonal antibody / Fab / HIV-1 / gp120 / third variable loop / antibody-antigen interaction / mimotope | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 3mls.cif.gz | 359.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mls.ent.gz | 302.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mls_validation.pdf.gz | 516.8 KB | Display | wwPDB validaton report |
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Full document | 3mls_full_validation.pdf.gz | 572.2 KB | Display | |
Data in XML | 3mls_validation.xml.gz | 76.7 KB | Display | |
Data in CIF | 3mls_validation.cif.gz | 106.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mls ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mls | HTTPS FTP |
-Related structure data
Related structure data | 3go1C 3mlrC 3mltC 3mluC 3mlvC 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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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) Homo sapiens (human) #2: Antibody | Mass: 24191.055 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) #3: Protein/peptide | Mass: 2084.402 Da / Num. of mol.: 4 / Source method: obtained synthetically #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: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 17% PEG4K, 8.5% 2-Propanol, 85mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9809 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2009 Details: Double crystal channel cut, Si(111), 1m long Rh coated toroidal mirror for vertical and horizontal focusing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9809 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→500 Å / Num. obs: 63477 / % possible obs: 90.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.078 / Χ2: 1.25 / Net I/σ(I): 9.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 40.21 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.26 Å2 / Biso mean: 28.021 Å2 / Biso min: 1.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Xplor file |
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