university lille north of france LigASite database of binding sites
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LigASite v3.0 (nr25) - non-redundant
LigASite v3.0 (redundant) - redundant
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apo-structureHelp

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

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4ape
HYDROLASE (ACID PROTEINASE) HEADER
THE ACTIVE SITE OF ASPARTIC PROTEINASES TITLE
ENDOTHIAPEPSIN COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

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

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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7 ILE
8 ASP
10 LEU
12 ASP
13 ALA
15 ASP
16 ALA
30 ASP
32 ASP
34 GLY
35 SER
73 ILE
74 SER
75 TYR
76 GLY
77 ASP
79 SER
81 ASP
110 SER
111 PHE
114 ASP
115 SER
116 PHE
117 ILE
119 ASP
120 LEU
122 ILE
128 LEU
130 THR
189 PHE
213 ILE
215 ASP
217 GLY
218 THR
219 THR
220 LEU
221 GLY
222 TYR
223 THR
224 LEU
226 TYR
275 PHE
280 PHE
284 PHE
291 PHE
296 GLY
297 ILE
299 ILE
301 ILE
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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
1epp LYSI___2 PHEI___3 STAI___1 MTFI___2 MBAI___2 MASI___4 47 233 Details
4er1 BNAI___1 25 83 Details
1eed BOCI___4 FOGI___3 CHSI___1 36 141 Details
1e82 CYMA___3 MRMA___1 PCHA___4 HFAA___2 46 172 Details
1od1 DPHB_401 TSMB_400 18 71 Details
1epq GCLI___1 17 85 Details
1e81 CPYA___4 MRMC___1 CYMA___3 HFAA___2 46 166 Details
v3.0
January 2008		 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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