university lille north of france LigASite database of binding sites
holo-structureHelp

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

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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.

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

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Links to external databases:

LigPlot (hosted at the EBI):

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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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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.

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apo-structure
pdb ID
1gsh 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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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
SO4 NAME: SULFATE ION
FORMULA: O4 S1
SMILES: [O-]S([O-])(=O)=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
GTT NAME: GLUTATHIONE
FORMULA: C10 H18 N3 O6 S1
SMILES: [NH3+]C(CCC(=O)NC(CS)C(=O)NCC(O)=O)C(O)=O
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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