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 ILE
17 GLY
18 LYS
19 ASN
20 GLY
21 ASP
22 LEU
24 TRP
26 PRO
27 LEU
28 ARG
30 GLU
31 PHE
32 ARG
33 TYR
34 PHE
35 GLN
52 MET
53 GLY
54 LYS
55 LYS
56 THR
59 SER
60 ILE
61 PRO
63 LYS
64 ASN
67 LEU
68 LYS
70 ARG
75 LEU
76 SER
77 ARG
78 GLU
79 LEU
90 SER
91 ARG
92 SER
93 LEU
115 VAL
116 GLY
117 GLY
118 SER
119 SER
120 VAL
121 TYR
123 GLU
136 THR
145 ASP
146 THR
147 PHE
150 GLU
179 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:

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
3nxv D2FA_187 NDPA_188 73 246 Details
3nxx D2DA_188 NDPA_187 73 249 Details
1pd8 CO4A_301 NDPA_300 76 293 Details
2dhf DZFB_187 32 149 Details
DZFA_187 32 145
1ohk COPA_188 NDPA_187 90 330 Details
3ghw GHWA_187 NDPA_188 79 299 Details
1ohj COPA_188 NDPA_187 90 340 Details
3nu0 3TUA_188 NDPA_187 84 310 Details
3ntz 3TZA_187 NDPA_188 83 293 Details
1s3v TQDA_187 27 123 Details
1dhf FOLB_187 32 139 Details
FOLA_187 32 140
3nxr D2DA_192 NDPA_187 72 246 Details
1s3u TQDA_187 27 126 Details
3s7a 684A_192 35 146 Details
1pd9 CO4A_187 28 127 Details
1kmv LIIA_201 NDPA_202 73 271 Details
1s3w NAPA_187 TQTA_188 70 259 Details
1kms LIHA_201 NDPA_202 73 278 Details
1drf FOLA_187 32 149 Details
3nxt SO4A_191 NDPA_187 53 188 Details
D2EA_188 SO4A_191 NDPA_187 77 268
1u72 MTXA_188 NDPA_187 81 315 Details
3nxy D2HA_188 NDPA_187 73 247 Details
3nzd D2QA_187 NDPA_188 80 289 Details
1hfr MOTA_188 NAPA_187 80 312 Details
1yho NDPA_190 TRRA_200 69 333 Details
2c2t 39BA1188 NDPA1187 69 243 Details
39BB1188 NDPB1187 69 252
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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