university lille north of france LigASite database of binding sites
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LigASite v4.0 (nr25) - non-redundant
LigASite v4.0 (redundant) - redundant
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apo-structureHelp

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

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2qgb
HORMONE/GROWTH FACTOR HEADER
HUMAN TRANSTHYRETIN (TTR) IN APO-FORM TITLE
TRANSTHYRETIN COMPND
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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13 MET
15 LYS
17 LEU
24 PRO
52 SER
54 GLU
56 HIS
106 THR
108 ALA
109 ALA
110 LEU
115 SER
116 TYR
117 SER
118 THR
119 THR
121 VAL
127 GLU
215 LYS
217 LEU
306 THR
308 ALA
309 ALA
310 LEU
317 SER
318 THR
319 THR
321 VAL
1013 MET
1015 LYS
1017 LEU
1106 THR
1108 ALA
1109 ALA
1110 LEU
1117 SER
1118 THR
1119 THR
1121 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.

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Links to external databases:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
holo-structuresHelp

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
2rox T44A_128 T44C_128 46 138 Details
T44B_128 T44D_128 46 145
1ict T44A_128 T44C_128 24 113 Details
T44B_129 T44D_129 24 116
1eta T44C_128 T44D_128 47 311 Details
2flm 6CAE_201 6CAF_201 64 261 Details
1bm7 FLFE_501 FLFF_501 36 111 Details
FLFE_502 FLFF_502 34 118
2roy P28A_128 P28C_128 54 171 Details
P28B_128 P28D_128 54 164
2qgd MR5A_200 MR5C_200 28 117 Details
MR5B_201 MR5D_201 28 119
2fbr 44CE_173 44CF_173 57 218 Details
2b77 3CAE_240 3CAF_240 30 105 Details
3CAE_239 3CAF_239 30 116
2gab NE2E_502 NE2F_502 28 106 Details
NE2E_501 NE2F_501 28 115
3b56 DIUA2000 DIUC2000 20 88 Details
DIUB3000 DIUD3000 21 96
2g5u NEWE_239 NEWF_239 30 106 Details
NEWE_240 NEWF_240 30 107
2qgc MR4B_128 MR4D_128 28 117 Details
MR4A_128 MR4C_128 29 115
2b9a FBCE_302 FBCF_302 29 128 Details
FBCE_301 FBCF_301 29 121
2qge MR6B_200 MR6D_200 31 114 Details
MR6A_201 MR6C_201 33 117
2b15 DNFE___1 DNFF___1 21 80 Details
DNFE___2 DNFF___2 21 81
1y1d FHIE3000 FHIF3000 33 132 Details
FHIE2000 FHIF2000 33 126
2f7i 26CE_326 26CF_326 29 105 Details
26CE_325 26CF_325 29 109
2g9k NE1E_501 NE1F_501 30 102 Details
NE1E_500 NE1F_500 30 98
1z7j T4AE_129 T4AF_129 41 132 Details
T4AE_128 T4AF_128 41 130
1tz8 DESC___1 DESD___1 20 99 Details
DESA___1 DESB___1 20 103
2f8i 205E1002 205F1002 35 130 Details
205E1001 205F1001 35 124
1tt6 DESE___1 DESF___1 35 122 Details
DESE___2 DESF___2 33 119
1u21 P2CE_221 P2CF_221 38 128 Details
P2CE_211 P2CF_211 36 136
v4.0
May 2008		 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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