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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16 PHE
28 ALA
29 SER
30 HIS
31 LYS
32 TRP
34 MET
35 ILE
38 LYS
39 GLU
41 THR
42 GLY
44 GLY
46 SER
47 VAL
48 ILE
49 MET
53 GLU
54 ALA
55 GLY
56 ILE
57 ASP
59 GLY
60 TYR
87 GLU
90 LEU
94 GLY
95 GLN
98 MET
99 THR
122 TYR
123 LYS
124 LEU
126 PHE
127 PHE
166 GLY
168 ASN
170 TYR
177 PRO
180 LEU
181 GLN
184 GLU
187 VAL
188 ASP
190 ILE
191 LYS
197 TYR
198 ALA
199 PRO
200 PHE
201 PRO
202 GLY
203 GLY
204 ILE
205 VAL
207 SER
208 ALA
209 SER
210 LYS
211 VAL
216 TYR
217 ASP
218 PHE
219 LEU
220 PRO
221 ALA
224 ASN
245 GLU
247 VAL
279 GLY
280 ASN
281 PHE
285 LEU
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
2fhk MFNC_600 31 143 Details
MFNH_602 31 132
2fhj MFNI_900 39 151 Details
PE4C_922 18 80
H4ZP_904 MFNR_903 50 213
PE4S_921 PE4T_920 __KB_503 43 197
H4ZB_905 MFNC_902 66 247
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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