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

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

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1sgz
HYDROLASE HEADER
CRYSTAL STRUCTURE OF UNBOUND BETA-SECRETASE CATALYTIC DOMAIN. TITLE
BETA-SECRETASE 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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9 LYS
10 SER
11 GLY
12 GLN
13 GLY
14 TYR
30 LEU
32 ASP
34 GLY
35 SER
36 SER
37 ASN
69 VAL
70 PRO
71 TYR
72 THR
73 GLN
74 GLY
75 LYS
76 TRP
106 ASP
107 LYS
108 PHE
110 ILE
115 TRP
118 ILE
126 ILE
128 ARG
154 LEU
198 TYR
224 LYS
226 ILE
228 ASP
229 SER
230 GLY
231 THR
232 THR
233 ASN
235 ARG
264 GLY
307 ARG
325 SER
329 THR
332 VAL
335 ALA
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:

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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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
3ufl 508P_449 GOLO_455 40 139 Details
508G_449 GOLF_455 40 135
2p4j 23IB_502 49 206 Details
23IC_503 49 193
23ID_504 49 201
23IA_501 49 194
1xs7 MMID_386 52 191 Details
2g94 ZPQB2001 45 172 Details
ZPQA1001 45 164
ZPQD4001 45 173
ZPQC3001 45 173
2vkm BSDD1386 47 200 Details
BSDA1386 47 207
BSDC1386 47 195
BSDB1386 47 199
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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