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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3kal
LIGASE HEADER
STRUCTURE OF HOMOGLUTATHIONE SYNTHETASE FROM GLYCINE MAX IN CLOSED CONFORMATION WITH HOMOGLUTATHIONE, ADP, A SULFATE ION, AND THREE MAGNESIUM IONS BOUND TITLE
HOMOGLUTATHIONE 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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HGS G 501
153G ARG
171G ASN
173G ILE
174G SER
175G THR
176G SER
177G PHE
238G GLN
241G GLU
243G ASN
295G ARG
298G TYR
392G GLU
393G GLY
475G ARG
485G GLY
486G VAL
487G LEU
488G PRO
SO4 H 505
153G ARG
155G ASP
169G GLU
171G ASN
392G GLU
393G GLY
394G GLY
475G ARG
HGS A 501
153A ARG
171A ASN
173A ILE
174A SER
175A THR
176A SER
177A PHE
238A GLN
241A GLU
243A ASN
247A GLN
295A ARG
298A TYR
392A GLU
393A GLY
475A ARG
485A GLY
486A VAL
487A LEU
488A PRO
SO4 B 505
153A ARG
169A GLU
171A ASN
392A GLU
393A GLY
394A GLY
475A ARG
MG F 503
155A ASP
169A GLU
450A GLU
475A ARG
MG L 503
155G ASP
169G GLU
475G ARG
ADP C 500
157A MET
168A ILE
169A GLU
334A LYS
386A VAL
388A LYS
392A GLU
393A GLY
394A GLY
395A GLY
396A ASN
397A ASN
399A TYR
424A MET
425A GLN
426A ARG
427A ILE
448A ILE
450A GLU
475A ARG
477A LYS
482A TYR
483A GLU
484A GLY
ADP I 500
157G MET
168G ILE
169G GLU
334G LYS
386G VAL
388G LYS
391G ARG
392G GLU
393G GLY
394G GLY
396G ASN
397G ASN
399G TYR
424G MET
425G GLN
426G ARG
427G ILE
448G ILE
450G GLU
475G ARG
477G LYS
482G TYR
483G GLU
484G GLY
MG E 502
169A GLU
171A ASN
392A GLU
MG K 502
169G GLU
171G ASN
392G 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):

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
3kaj Details
other holo-structures
pdb ID Ligand Unique ID
3kak 3GCE_501 Details
3GCB_501
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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HGS NAME: not_found
FORMULA: not_found
SMILES: not_found
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
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