university lille north of france LigASite database of binding sites
Home
News
Introduction
Methods
Flow Chart
References
Download
About
FAQ
Search
LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
(click to remove window)
Browse dataset
holo-structureHelp

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

(click anywhere in this window to remove it)
1gsa
LIGASE HEADER
STRUCTURE OF GLUTATHIONE SYNTHETASE COMPLEXED WITH ADP AND GLUTATHIONE TITLE
GLUTATHIONE SYNTHETASE 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
GTT C 318
9A ASP
18A LYS
19A ASP
20A SER
21A SER
86A ARG
88A ASP
89A PRO
124A GLU
165A MET
166A GLY
210A ARG
225A ARG
235A ASN
236A LEU
237A ALA
283A ASN
285A THR
286A SER
287A PRO
288A THR
289A CYS
GTT I 318
18G LYS
19G ASP
20G SER
21G SER
86G ARG
88G ASP
89G PRO
124G GLU
165G MET
166G GLY
210G ARG
225G ARG
235G ASN
236G LEU
237G ALA
283G ASN
285G THR
286G SER
287G PRO
288G THR
289G CYS
MG K 320
124G GLU
165G MET
281G GLU
283G ASN
MG E 320
124A GLU
165A MET
281A GLU
283A ASN
ADP J 317
125G LYS
136G PRO
158G ILE
160G LYS
164G GLY
165G MET
167G GLY
168G ALA
170G ILE
198G GLN
199G ASN
200G TYR
201G LEU
204G ILE
208G ASP
232G THR
233G ARG
234G GLY
235G ASN
273G ASP
275G ILE
280G THR
281G GLU
ADP D 317
125A LYS
136A PRO
158A ILE
160A LYS
164A GLY
165A MET
167A GLY
168A ALA
170A ILE
198A GLN
199A ASN
200A TYR
201A LEU
204A ILE
208A ASP
232A THR
233A ARG
234A GLY
235A ASN
273A ASP
275A ILE
280A THR
281A GLU
SO4 H 400
165G MET
166G GLY
210G ARG
225G ARG
235G ASN
273G ASP
281G GLU
283G ASN
SO4 B 400
165A MET
166A GLY
210A ARG
225A ARG
235A ASN
273A ASP
281A GLU
283A ASN
MG L 319
208G ASP
225G ARG
235G ASN
273G ASP
281G GLU
MG F 319
208A ASP
225A ARG
235A ASN
273A ASP
281A GLU
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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
Hide table of related structures
Help

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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
2glt 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.

(click anywhere in this window to remove it)
GTT NAME: GLUTATHIONE
FORMULA: C10 H18 N3 O6 S1
SMILES: [NH3+]C(CCC(=O)NC(CS)C(=O)NCC(O)=O)C(O)=O
SO4 NAME: SULFATE ION
FORMULA: O4 S1
SMILES: [O-]S([O-])(=O)=O
ADP NAME: ADENOSINE-5'-DIPHOSPHATE
FORMULA: C10 H15 N5 O10 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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
Script execution time: 0.097 seconds