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Yorodumi- PDB-1lec: STRUCTURES OF THE LECTIN IV OF GRIFFONIA SIMPLICIFOLIA AND ITS CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lec | ||||||||||||
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Title | STRUCTURES OF THE LECTIN IV OF GRIFFONIA SIMPLICIFOLIA AND ITS COMPLEX WITH THE LEWIS B HUMAN BLOOD GROUP DETERMINANT AT 2.0 ANGSTROMS RESOLUTION | ||||||||||||
Components | WEST-CENTRAL AFRICAN LEGUME LECTIN IV | ||||||||||||
Keywords | LECTIN | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Griffonia simplicifolia (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||||||||
Authors | Delbaere, L. / Vandonselaar, M. / Quail, 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: 1990 Title: Molecular Recognition of a Human Blood Group Determinant by a Plant Lectin Authors: Delbaere, L.T.J. / Vandonselaar, M. / Prasad, L. / Quail, J.W. / Pearlstone, J.R. / Carpenter, M.R. / Smillie, L.B. / Nikrad, P.V. / Spohr, U. / Lemieux, R.U. #2: Journal: Trans.Am.Crystallogr.Assoc. / Year: 1991 Title: Structures of Griffonia Simplicifolia Lectin Iv and its Complex with a Synthetic Lewis B Blood Group Determinant Authors: Delbaere, L.T.J. / Vandonselaar, M. / Prasad, L. / Quail, J.W. / Nikrad, P.V. / Pearlstone, J.R. / Carpenter, M.R. / Smillie, L.B. / Spohr, U. / 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 | 1lec.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lec.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lec_validation.pdf.gz | 901.4 KB | Display | wwPDB validaton report |
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Full document | 1lec_full_validation.pdf.gz | 905.9 KB | Display | |
Data in XML | 1lec_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1lec_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1lec ftp://data.pdbj.org/pub/pdb/validation_reports/le/1lec | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 86 IS A CIS PROLINE. 2: PEPTIDE BONDS ALA 88 - ASP 89 AND VAL 221 - GLY 222 ARE CIS PEPTIDE BONDS AND ARE INVOLVED IN CARBOHYDRATE BINDING SITE. 3: WATERS 403 AND 404 OCCUPY SPECIAL POSITIONS AND ARE SHARED BY TWO SYMMETRY RELATED MOLECULES. | |||||||||
Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 26816.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Griffonia simplicifolia (plant) / References: UniProt: P24146 |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 146 molecules
#3: Chemical | ChemComp-MN / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.2 / Method: vapor diffusion, hanging dropDetails: Vandonselaar,M., (1987) J. Biol. Chem., 262, 10848. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Highest resolution: 2 Å Details: RESIDUES 1 AND 241 - 243 HAVE VERY HIGH TEMPERATURE FACTORS AND ARE NOT WELL DETERMINED.
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Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor all: 0.187 / Num. reflection obs: 19204 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |