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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2io9
LIGASE, HYDROLASE HEADER
E. COLI BIFUNCTIONAL GLUTATHIONYLSPERMIDINE SYNTHETASE/AMIDASE INCOMPLEX WITH MG2+ ,GSH 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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GSH H5002
241F ASN
316F ARG
332F ASN
335F SER
336F ALA
337F SER
338F CYS
341F GLU
391F GLU
394F TYR
538F ARG
539F CYS
598F ARG
605F ILE
606F LYS
607F LYS
608F GLU
611F ILE
GSH C5001
241A ASN
316A ARG
332A ASN
335A SER
336A ALA
337A SER
338A CYS
341A GLU
391A GLU
394A TYR
538A ARG
539A CYS
598A ARG
606A LYS
607A LYS
608A GLU
611A ILE
MG J7004
316F ARG
318F ASP
330F GLU
332F ASN
582F GLN
605F ILE
MG E7002
316A ARG
318A ASP
330A GLU
332A ASN
582A GLN
ADP G3002
318F ASP
329F TYR
330F GLU
498F LYS
515F LEU
531F ALA
533F LYS
537F GLY
538F ARG
539F CYS
540F GLY
541F SER
543F ILE
545F LEU
568F GLN
569F GLN
570F LEU
571F TRP
572F CYS
573F LEU
582F GLN
603F LEU
604F VAL
605F ILE
ADP B3001
318A ASP
329A TYR
330A GLU
498A LYS
515A LEU
531A ALA
533A LYS
534A PRO
537A GLY
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 I7003
330F GLU
332F ASN
498F LYS
537F GLY
538F ARG
MG D7001
330A GLU
332A ASN
498A LYS
537A GLY
538A ARG
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
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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).

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apo-structure
pdb ID
2iob Details
other holo-structures
pdb ID Ligand Unique ID
2io7 ANPF_965 _MGH5004 _MGG5003 Details
ANPB_964 _MGC5001 _MGD5002
2ioa ADPB3001 _MGE5002 GGAC6001 _MGD5001 Details
ADPG3002 _MGI5003 _MGJ5004 GGAH6002
2io8 ADPF5002 _MGH7004 _MGG7003 Details
ADPB5001 _MGD7002 _MGC7001
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++]
GSH NAME: GLUTATHIONE
FORMULA: C10 H17 N3 O6 S1
SMILES: NC(CCC(=O)NC(CS)C(=O)NCC(O)=O)C(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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