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Yorodumi- PDB-1gsl: LECTIN (FOURTH ISOLATED FROM (GRIFFONIA SIMPLICIFOLIA)) COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gsl | ||||||||||||
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Title | LECTIN (FOURTH ISOLATED FROM (GRIFFONIA SIMPLICIFOLIA)) COMPLEX WITH Y HUMAN BLOOD GROUP DETERMINANT | ||||||||||||
Components | GRIFFONIA SIMPLICIFOLIA LECTIN 4 | ||||||||||||
Keywords | LECTIN / GLYCOPROTEIN / MANGANESE | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Griffonia simplicifolia (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||||||||
Authors | Delbaere, L.T.J. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Structures of the lectin IV of Griffonia simplicifolia and its complex with the Lewis b human blood group determinant at 2.0 A resolution. Authors: Delbaere, L.T. / Vandonselaar, M. / Prasad, L. / Quail, J.W. / Wilson, K.S. / Dauter, Z. #1: Journal: Can.J.Chem. / Year: 1985 Title: Molecular Recognition. II. The Binding of the Lewis B and Y Human Blood Group Determinants by the Lectin Iv of Griffonia Simplicifolia Authors: Spohr, U. / Hindsgaul, O. / Lemieux, R.U. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gsl.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gsl.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gsl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1gsl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1gsl_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1gsl_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/1gsl ftp://data.pdbj.org/pub/pdb/validation_reports/gs/1gsl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26816.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Griffonia simplicifolia (plant) / Organ: SEEDS / References: UniProt: P24146 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]methyl 2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 165 molecules
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | PEPTIDE BOND VAL 221 - GLY 222 IS A CIS PEPTIDE BOND AND IS INVOLVED IN CARBOHYDRA |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Vandonselaar,M., (1987) J. Biol. Chem., 262, 10848. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 2, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 16584 / % possible obs: 83.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Resolution: 2→40 Å / σ(F): 0 Details: RESIDUES 1 AND 241 - 243 HAVE VERY HIGH TEMPERATURE FACTORS AND ARE NOT WELL DETERMINED.
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Displacement parameters | Biso mean: 31.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2423 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |