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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22 PHE
23 ARG
26 LEU
27 SER
31 THR
33 VAL
41 PRO
42 PHE
47 LEU
48 THR
49 CYS
50 SER
51 ALA
54 SER
55 VAL
56 CYS
57 ASP
58 ARG
65 CYS
66 ILE
67 ASN
69 LYS
70 SER
71 TYR
72 ALA
77 LYS
78 SER
79 ASN
80 GLY
81 VAL
95 SER
96 GLN
98 PHE
99 ALA
100 GLY
103 SER
104 VAL
105 PRO
106 MET
109 ARG
135 THR
136 ILE
137 ALA
144 SER
145 HIS
166 TYR
169 ARG
171 TYR
1022 PHE
1023 ARG
1026 LEU
1027 SER
1031 THR
1033 VAL
1047 LEU
1048 THR
1049 CYS
1050 SER
1051 ALA
1054 SER
1055 VAL
1056 CYS
1057 ASP
1065 CYS
1066 ILE
1067 ASN
1069 LYS
1070 SER
1095 SER
1096 GLN
1098 PHE
1099 ALA
1100 GLY
1101 VAL
1144 SER
1145 HIS
1166 TYR
1169 ARG
1171 TYR
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
3k88 FADK_500 NADL_501 97 237 Details
FADB1500 NADC1501 97 238
FADN1500 NADO1501 97 238
FADH1500 NADI1501 97 241
FADQ_500 NADR_501 97 238
FADE_500 NADF_501 97 239
3k87 FADB_600 53 104 Details
FADD_500 53 149
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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