university lille north of france LigASite database of binding sites

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

(click anywhere in this window to remove it)
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).

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
10 CYS
11 SER
12 SER
13 GLY
14 ILE
15 GLY
35 THR
36 LEU
37 ARG
38 ASP
41 THR
44 ARG
64 LEU
65 ASP
66 VAL
67 ARG
89 CYS
90 ASN
91 ALA
92 GLY
93 LEU
94 GLY
95 LEU
96 LEU
113 VAL
140 THR
141 GLY
142 SER
143 VAL
144 GLY
147 MET
149 LEU
150 PRO
152 ASN
155 TYR
156 CYS
159 LYS
162 LEU
185 CYS
186 GLY
187 PRO
188 VAL
189 HIS
190 THR
191 ALA
192 PHE
193 MET
194 GLU
196 VAL
218 TYR
221 HIS
222 SER
225 VAL
226 PHE
258 ARG
259 PHE
262 LEU
279 MET
282 GLU
283 VAL
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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
pdb ID Ligand Unique ID #atoms #contacts
3dhe ANDB_400 21 82 Details
ANDD_400 21 86
3dey DHTB_732 21 85 Details
DHTE_732 21 86
1qyw 5SDG_500 21 88 Details
5SDC_500 21 83
NAPF_361 27 111
NAPB_361 27 107
3km0 AOMF___1 NAPE_360 69 223 Details
AOMC___1 NAPB_360 69 239
1qyx ASDD_500 21 83 Details
NAPF_361 27 111
ASDH_500 21 83
NAPB_361 27 108
1dht DHTD_400 21 84 Details
DHTB_400 21 90
3klp B81A_328 21 92 Details
B81B_328 21 90
1jtv TESB_500 21 75 Details
TESE_500 21 81
1equ EQIC_329 NAPB_328 68 256 Details
NAPE_328 48 178
3hb4 E2BB_700 30 138 Details
E2BA_700 30 139
1qyv NAPE_361 48 162 Details
NAPB_361 48 164
3hb5 NAPD_360 48 171 Details
NAPB_360 48 169
E2BC_700 30 121
E2BA_700 30 123
1i5r GOLG_401 HYCF_328 55 247 Details
GOLC_401 HYCB_328 55 242
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
Script execution time: 0.089 seconds