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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1mr7
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF STREPTOGRAMIN A ACETYLTRANSFERASE TITLE
STREPTOGRAMIN A ACETYLTRANSFERASE 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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11 ILE
14 ASN
16 SER
17 VAL
37 TYR
39 ASP
52 TYR
54 TYR
56 ILE
57 LEU
68 SER
69 ILE
70 GLY
71 PRO
76 ILE
79 GLY
80 ALA
81 ASN
82 HIS
83 ARG
84 MET
90 PRO
92 ASN
93 LEU
102 MET
103 PRO
105 LEU
108 LEU
109 PRO
111 LYS
121 TRP
122 ILE
123 GLY
124 LYS
129 MET
130 PRO
139 ILE
140 VAL
141 ALA
142 ALA
144 SER
145 VAL
147 VAL
148 LYS
155 LEU
157 GLY
158 GLY
159 ASN
160 PRO
162 ASN
164 ILE
165 LYS
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
1mrl DOLD_302 48 120 Details
DOLD_301 48 145
DOLD_300 48 121
1mr9 ACOB_301 ACOC_301 51 173 Details
ACOA_300 ACOB_300 51 161
ACOA_302 ACOC_302 51 142
1khr COAE_305 48 172 Details
COAD_304 VIRD_403 86 273
COAD_306 COAF_306 48 168
1kk4 ACOE_305 51 180 Details
ACOD_304 51 188
ACOD_306 51 186
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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