university lille north of france LigASite database of binding sites

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

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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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21 THR
26 TYR
36 PHE
37 ASP
42 ARG
44 LYS
46 PHE
47 LYS
48 PHE
49 MET
52 LYS
53 GLN
54 GLU
55 VAL
56 ILE
57 ARG
59 TRP
78 PRO
79 ASP
80 TYR
81 ALA
82 TYR
83 GLY
85 THR
86 GLY
87 HIS
88 PRO
89 GLY
90 ILE
91 ILE
97 LEU
99 PHE
207 ILE
208 SER
209 PRO
226 TYR
236 PHE
237 ASP
242 ARG
246 PHE
253 GLN
254 GLU
255 VAL
256 ILE
259 TRP
271 ARG
281 ALA
282 TYR
283 GLY
284 ALA
285 THR
287 HIS
288 PRO
290 ILE
291 ILE
299 PHE
302 GLU
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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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 RAPA_501 65 133 Details
1f40 GPIA_108 26 117 Details
1nsg RADA_108 66 225 Details
1qpl 587A_108 67 149 Details
587C_308 67 115
1qpf 858D_108 B7GG_109 858J_308 858E_308 B7GB_109 858I_108 306 729 Details
B7GG_109 858E_308 858I_108 153 363
1fkb RAPA_108 65 123 Details
1a7x FKAB_201 67 179 Details
3fap ARDA_402 69 222 Details
2fap RADA_108 66 222 Details
1j4h SUBA_201 32 95 Details
1fkh SBXA_108 33 106 Details
2fke FK5F_108 FK5D_108 FK5H_108 171 448 Details
FK5B_108 FK5F_108 FK5D_108 FK5H_108 228 602
1j4i TSTA_201 27 86 Details
1fkd 818B_108 818D_108 114 312 Details
818F_108 818H_108 114 316
1fkg SB3A_108 33 97 Details
1fap RAPA_108 65 223 Details
1fkf FK5B_108 FK5F_108 FK5D_108 FK5H_108 228 619 Details
1fki SB1B_108 31 96 Details
SB1A_109 31 97
1j4r 001B_109 45 131 Details
001A_108 45 119
001D_109 45 126
4fap ARDA_402 69 238 Details
1fkj FK5B_108 FK5F_108 FK5D_108 FK5H_108 228 623 Details
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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