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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1ulf
SUGAR BINDING PROTEIN HEADER
CGL2 IN COMPLEX WITH BLOOD GROUP A TETRASACCHARIDE TITLE
GALECTIN-2 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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A2G D 151
36A THR
38A VAL
40A ASN
51A HIS
53A SER
55A ARG
66A ARG
72A TRP
126A ASN
127A ALA
A2G N 151
36K THR
38K VAL
40K ASN
51K HIS
53K SER
66K ARG
72K TRP
126K ASN
127K ALA
A2G I 151
36F THR
38F VAL
40F ASN
51F HIS
53F SER
55F ARG
66F ARG
72F TRP
126F ASN
127F ALA
A2G S 151
36P THR
38P VAL
40P ASN
51P HIS
53P SER
66P ARG
72P TRP
126P ASN
127P ALA
GAL B 152
51A HIS
53A SER
55A ARG
62A VAL
64A ASN
72A TRP
75A GLU
GAL L 152
51K HIS
53K SER
55K ARG
62K VAL
64K ASN
72K TRP
75K GLU
GAL G 152
51F HIS
53F SER
55F ARG
62F VAL
64F ASN
72F TRP
75F GLU
GAL Q 152
51P HIS
53P SER
55P ARG
62P VAL
64P ASN
72P TRP
75P GLU
BGC C 153
55A ARG
58A GLU
72A TRP
75A GLU
77A ARG
FUC E 154
55A ARG
58A GLU
BGC M 153
55K ARG
58K GLU
72K TRP
75K GLU
77K ARG
FUC O 154
55K ARG
58K GLU
FUC J 154
55F ARG
58F GLU
BGC H 153
55F ARG
58F GLU
72F TRP
75F GLU
77F ARG
BGC R 153
55P ARG
58P GLU
72P TRP
75P GLU
77P ARG
FUC T 154
55P ARG
58P GLU
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).

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apo-structure
pdb ID
1ul9 Details
other holo-structures
pdb ID Ligand Unique ID
1ule GALJ_152 GLAK_151 NAGL_153 Details
GALF_152 NAGH_153 GLAG_151
GALN_152 GLAO_151 NAGP_153
GALB_152 NAGD_153 GLAC_151
1uld FUCP_153 NAGO_152 GALN_151 Details
FUCL_153 GALJ_151 NAGK_152
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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A2G NAME: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
BGC NAME: BETA-D-GLUCOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
FUC NAME: FUCOSE
FORMULA: C6 H12 O5
SMILES: CC1OC(O)C(O)C(O)C1O
GAL NAME: D-GALACTOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)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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