university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1y2v
SUGAR BINDING PROTEIN HEADER
CRYSTAL STRUCTURE OF THE COMMON EDIBLE MUSHROOM (AGARICUS BISPORUS) LECTIN IN COMPLEX WITH T-ANTIGEN TITLE
LECTIN COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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GAL B 145
28A TYR
29A ALA
30A ASN
48A SER
49A GLY
NGA C 144
28A TYR
48A SER
49A GLY
72A HIS
73A ASN
74A TYR
98A TYR
107A ARG
GAL E 145
28D TYR
29D ALA
30D ASN
48D SER
49D GLY
NGA F 144
28D TYR
48D SER
49D GLY
72D HIS
73D ASN
74D TYR
98D TYR
107D ARG
GAL K 145
28J TYR
29J ALA
30J ASN
48J SER
49J GLY
NGA L 144
28J TYR
48J SER
49J GLY
72J HIS
73J ASN
74J TYR
98J TYR
107J ARG
GAL H 145
28G TYR
29G ALA
30G ASN
48G SER
49G GLY
NGA I 144
28G TYR
48G SER
49G GLY
72G HIS
73G ASN
74G TYR
98G TYR
107G ARG
SER A 146
72A HIS
73A ASN
SER D 146
72D HIS
73D ASN
SER J 146
72J HIS
73J ASN
SER G 146
72G HIS
73G ASN
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

LigPlot (hosted at the EBI):

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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Hide table of related structures
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List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1y2t Details
other holo-structures
pdb ID Ligand Unique ID
1y2x GALF_146 NGAG_145 SERE_147 Details
GALL_146 SERK_147 NGAM_145
GALB_146 NGAD_145 SERA_147
GALI_146 NGAJ_145 SERH_147
1y2w GALF_145 NGAG_144 SERE_146 Details
GALM_145 NGAN_144 SERL_146
GALI_145 SERH_146 NGAK_144
GALB_145 SERA_146 NGAD_144
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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GAL NAME: D-GALACTOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
SER NAME: L-Serine
FORMULA: C3 H6 N1 O3
SMILES: NC(CO)C(O)=OSERINE
NGA NAME: N-ACETYL-D-GALACTOSAMINE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
v9.7
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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