university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (redundant) - redundant
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apo-structureHelp

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

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2pt7
HYDROLASE/PROTEIN BINDING HEADER
CRYSTAL STRUCTURE OF CAG VIRB11 (HP0525) AND AN INHIBITORY PROTEIN (HP1451) TITLE
CAG-ALFA 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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38 ASP
39 PHE
41 LYS
43 GLU
44 ASN
45 ILE
46 THR
55 VAL
61 ASN
67 PRO
68 PHE
69 ASP
70 VAL
71 ARG
73 ARG
113 ARG
133 ARG
134 ILE
135 PRO
136 SER
137 LYS
138 THR
140 TYR
144 PHE
145 PHE
148 GLN
150 PHE
180 THR
181 GLY
182 SER
183 GLY
184 LYS
185 THR
186 THR
209 GLU
247 GLY
248 GLU
271 THR
273 HIS
320 LYS
1038 ASP
1039 PHE
1041 LYS
1043 GLU
1055 VAL
1067 PRO
1068 PHE
1069 ASP
1070 VAL
1071 ARG
1073 ARG
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
1g6o PEGI_500 PEGI_503 PEGI_504 PEGI_502 PEGI_501 28 82 Details
ADPH_401 27 136
PEGG_500 PEGG_503 PEGG_502 PEGG_504 PEGG_501 28 86
ADPI_401 27 136
ADPG_402 27 138
ADPH_402 27 141
ADPG_401 27 136
ADPI_402 27 138
PEGH_500 PEGH_502 PEGH_504 PEGH_503 PEGH_501 28 83
1opx 2PEI2000 28 81 Details
2PEH2000 28 80
2PEG2000 28 82
1nly ATGG_400 _MGG_700 32 153 Details
2PEG_600 28 70
ATGI_500 SO4I_800 36 154
2PEI_600 28 74
ATGI_400 _MGI_700 32 151
ATGH_500 SO4H_800 36 151
2PEH_600 28 74
ATGG_500 SO4G_800 36 152
ATGH_400 _MGH_700 32 148
v6.0
October 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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