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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1uih
HYDROLASE HEADER
ANALYSIS OF THE STABILIZATION OF HEN LYSOZYME WITH THE HELIX DIPOLE AND CHARGED SIDE CHAINS TITLE
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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NAG A 503
48A ASP
52A ASP
56A LEU
57A GLN
58A ILE
59A ASN
61A ARG
62A TRP
63A TRP
98A ILE
107A ALA
108A TRP
NAG A 501
62A TRP
73A ARG
75A LEU
101A ASP
102A GLY
103A ASN
NAG A 502
62A TRP
63A TRP
75A LEU
101A ASP
103A 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
Help

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
1vdq Details
other holo-structures
pdb ID Ligand Unique ID
2fbb NO3F_158 NO3L_158 _NAR_132 NO3T_150 NO3S_150 Details
1jj0 SUCA2380 Details
1sfb NAGA_201 NAGA_202 NAGA_203 NAGA_205 NAGA_204 Details
2znx 1PGB_243 Details
1PGA_243
1hew NAGA_201 NAGA_202 NAGA_203 Details
1sf7 NAGA_201 NAGA_202 NAGA_203 NAGA_204 Details
3sp3 SUCA_130 Details
1sf4 NAGA_201 NAGA_202 Details
1sf6 NAGA_201 NAGA_202 NAGA_203 NAGA_204 Details
1uc0 GALA_130 GOLA_132 NAGA_131 Details
2znw 1PGB_243 Details
1PGA_243
1lzc NAGA_130 NAGA_132 NAGA_131 Details
1sfg NAGA_201 NAGA_202 NAGA_203 NAGA_205 NAGA_204 Details
1at5 NAGA_132 NAGA_131 Details
NAGA_130 NAGA_132 NAGA_131
2hub EDOA1001 EPEA2001 Details
1lzb NAGA_132 NAGA_131 Details
NAGA_130 NAGA_132 NAGA_131
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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NAG NAME: N-ACETYL-D-GLUCOSAMINE
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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