university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

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

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1a69
GLYCOSYLTRANSFERASE HEADER
PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH FORMYCIN B AND SULPHATE (PHOSPHATE) TITLE
PURINE NUCLEOSIDE PHOSPHORYLASE COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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FMB F 240
4P HIS
43P ARG
64D MET
71P ILE
87D ARG
90D SER
91D CYS
92D GLY
156D ALA
159D PHE
178D VAL
179D GLU
180D MET
181D GLU
203D SER
204D ASP
206D ILE
217D ARG
FMB L 240
4A HIS
43A ARG
63J GLY
64J MET
71A ILE
87J ARG
90J SER
91J CYS
92J GLY
156J ALA
159J PHE
178J VAL
179J GLU
180J MET
181J GLU
203J SER
204J ASP
206J ILE
FMB C 240
4J HIS
43J ARG
64A MET
71J ILE
87A ARG
90A SER
91A CYS
92A GLY
156A ALA
159A PHE
178A VAL
179A GLU
180A MET
181A GLU
203A SER
204A ASP
206A ILE
217A ARG
FMB R 240
4D HIS
43D ARG
64P MET
71D ILE
87P ARG
90P SER
91P CYS
92P GLY
156P ALA
159P PHE
178P VAL
179P GLU
180P MET
181P GLU
203P SER
204P ASP
206P ILE
FMB O 240
4G HIS
43G ARG
64M MET
71G ILE
87M ARG
90M SER
91M CYS
92M GLY
156M ALA
159M PHE
178M VAL
179M GLU
180M MET
181M GLU
203M SER
204M ASP
206M ILE
FMB I 240
4M HIS
43M ARG
64G MET
71M ILE
87G ARG
90G SER
91G CYS
92G GLY
156G ALA
159G PHE
178G VAL
179G GLU
180G MET
181G GLU
203G SER
204G ASP
206G ILE
SO4 K 239
19J PRO
20J GLY
21J ASP
43A ARG
87J ARG
88J VAL
89J GLY
90J SER
SO4 Q 239
19P PRO
20P GLY
21P ASP
43D ARG
87P ARG
88P VAL
89P GLY
90P SER
181P GLU
SO4 E 239
20D GLY
24D ARG
43P ARG
87D ARG
89D GLY
90D SER
SO4 B 239
20A GLY
24A ARG
43J ARG
87A ARG
89A GLY
90A SER
SO4 N 239
20M GLY
24M ARG
43G ARG
64M MET
87M ARG
89M GLY
90M SER
SO4 H 239
20G GLY
24G ARG
43M ARG
64G MET
87G ARG
89G GLY
90G SER
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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 binding site (PDB)
Hide table of related structures
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List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1ecp Details
other holo-structures
pdb ID Ligand Unique ID
none
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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FMB NAME: FORMYCIN B
FORMULA: C10 H12 N4 O5
SMILES: OCC1OC(C(O)C1O)c2n[nH]c3C(=O)NC=Nc23
SO4 NAME: SULFATE ION
FORMULA: O4 S1
SMILES: [O-]S([O-])(=O)=O
v9.7
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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