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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2io8
LIGASE, HYDROLASE HEADER
E. COLI BIFUNCTIONAL GLUTATHIONYLSPERMIDINE SYNTHETASE/AMIDASE INCOMPLEX WITH MG2+ AND ADP TITLE
BIFUNCTIONAL GLUTATHIONYLSPERMIDINE 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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MG H7004
316E ARG
318E ASP
330E GLU
332E ASN
582E GLN
605E ILE
MG D7002
316A ARG
318A ASP
330A GLU
332A ASN
582A GLN
605A ILE
ADP F5002
318E ASP
329E TYR
330E GLU
498E LYS
515E LEU
531E ALA
533E LYS
537E GLY
538E ARG
539E CYS
540E GLY
541E SER
543E ILE
545E LEU
568E GLN
569E GLN
570E LEU
571E TRP
572E CYS
573E LEU
582E GLN
603E LEU
604E VAL
605E ILE
ADP B5001
318A ASP
329A TYR
330A GLU
498A LYS
515A LEU
531A ALA
533A LYS
538A ARG
539A CYS
540A GLY
541A SER
543A ILE
545A LEU
568A GLN
569A GLN
570A LEU
571A TRP
572A CYS
573A LEU
582A GLN
603A LEU
604A VAL
605A ILE
MG G7003
330E GLU
332E ASN
498E LYS
537E GLY
538E ARG
539E CYS
MG C7001
330A GLU
332A ASN
498A LYS
537A GLY
538A ARG
539A CYS
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).

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apo-structure
pdb ID
2iob Details
other holo-structures
pdb ID Ligand Unique ID
2io9 ADPG3002 _MGJ7004 GSHH5002 _MGI7003 Details
ADPB3001 _MGE7002 _MGD7001 GSHC5001
2io7 ANPF_965 _MGH5004 _MGG5003 Details
ANPB_964 _MGC5001 _MGD5002
2ioa ADPB3001 _MGE5002 GGAC6001 _MGD5001 Details
ADPG3002 _MGI5003 _MGJ5004 GGAH6002
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
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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