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- PDB-1s3k: Crystal Structure of a Humanized Fab (hu3S193) in Complex with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s3k | |||||||||
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Title | Crystal Structure of a Humanized Fab (hu3S193) in Complex with the Lewis Y Tetrasaccharide | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ramsland, P.A. / Farrugia, W. / Bradford, T.M. / Hogarth, P.M. / Scott, A.M. | |||||||||
![]() | ![]() Title: Structural convergence of antibody binding of carbohydrate determinants in lewis y tumor antigens Authors: Ramsland, P.A. / Farrugia, W. / Bradford, T.M. / Hogarth, P.M. / Scott, A.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.3 KB | Display | ![]() |
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PDB format | ![]() | 79 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1clyS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 24066.689 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: murine complementarity determining regions grafted onto human framework and constant sequences Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23796.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: murine complementarity determining regions grafted onto human framework and constant sequences Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis Y antigen / alpha anomer |
#4: Chemical | ChemComp-GOL / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.35 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 20000, sodium chloride, Tris, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→50 Å / Num. all: 39562 / Num. obs: 39562 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.062 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 3008 / Rsym value: 0.153 / % possible all: 73.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1CLY Resolution: 1.9→33.34 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.6 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→33.34 Å
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Refine LS restraints |
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