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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1re2
LYSOZYME HEADER
HUMAN LYSOZYME LABELLED WITH TWO 2',3'-EPOXYPROPYL BETA- GLYCOSIDE OF N-ACETYLLACTOSAMINE TITLE
PROTEIN (LYSOZYME) 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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GOL A 136
35A GLU
53A ASP
58A GLN
109A TRP
110A VAL
111A ALA
NAG A 134
46A ASN
104A GLN
107A ARG
108A ALA
109A TRP
110A VAL
113A ARG
NAG A 132
49A ASP
58A GLN
59A ILE
60A ASN
63A TYR
64A TRP
99A VAL
104A GLN
108A ALA
109A TRP
GOL A 135
53A ASP
58A GLN
60A ASN
GAL A 131
63A TYR
64A TRP
74A VAL
76A ALA
102A ASP
103A PRO
104A GLN
GAL A 133
104A GLN
107A ARG
113A ARG
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
1jwr Details
other holo-structures
pdb ID Ligand Unique ID
1rez GALA_131 NAGA_132 GOLA_133 Details
1rem BMAA_131 NAGA_132 PGRA_134 Details
1lzs NAGB_136 NAGB_138 NAGB_137 Details
NAGA_136 NAGA_139 NAGA_138 NAGA_137 NAGA_140 NAGA_141
1rey GOLA_133 NAGA_132 NAGA_131 Details
1lzr NAGA_136 NAGA_138 NAGA_137 Details
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
NAG NAME: N-ACETYL-D-GLUCOSAMINE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
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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