university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (redundant) - redundant
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apo-structureHelp

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

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2ppn
ISOMERASE HEADER
CRYSTAL STRUCTURE OF FKBP12 TITLE
FK506-BINDING PROTEIN 1A 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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26 TYR
36 PHE
37 ASP
42 ARG
44 LYS
46 PHE
47 LYS
48 PHE
53 GLN
54 GLU
55 VAL
56 ILE
57 ARG
59 TRP
78 PRO
79 ASP
80 TYR
81 ALA
82 TYR
83 GLY
84 ALA
85 THR
86 GLY
87 HIS
88 PRO
90 ILE
91 ILE
99 PHE
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
2dg3 RAPB_501 65 133 Details
1j4i TSTB_201 27 86 Details
1f40 GPI__108 26 97 Details
1nsg RPXA_108 65 126 Details
1fkd 818A_108 818B_108 114 268 Details
1fkg SB3__108 33 97 Details
1fkb RAP____1 65 123 Details
1a7x FKAE_201 FKAF_201 130 394 Details
1fkf FK5A_108 FK5B_108 114 259 Details
1fap RAPC_108 65 223 Details
1j4h SUBB_201 32 95 Details
1fkh SBX__108 33 106 Details
2fke FK5A_108 FK5B_108 114 255 Details
1j4r 001I___1 45 119 Details
1fki SB1C_109 31 97 Details
SB1C_108 31 96
1fkj FK5A_108 FK5B_108 114 260 Details
v6.0
October 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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