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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2ywc
LIGASE HEADER
CRYSTAL STRUCTURE OF GMP SYNTHETASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH XMP TITLE
GMP SYNTHASE [GLUTAMINE-HYDROLYZING] 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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XMP F 702
288E ARG
380E PRO
381E PHE
382E PRO
383E GLY
384E PRO
424E GLN
458E PHE
495E LYS
499E THR
500E ILE
501E GLU
503E GLU
XMP B 701
288A ARG
380A PRO
381A PHE
382A PRO
383A GLY
384A PRO
424A GLN
458A PHE
495A LYS
499A THR
500A ILE
501A GLU
503A GLU
XMP H 704
288G ARG
380G PRO
381G PHE
382G PRO
383G GLY
384G PRO
388G VAL
424G GLN
458G PHE
495G LYS
499G THR
500G ILE
501G GLU
503G GLU
XMP D 703
288C ARG
380C PRO
381C PHE
382C PRO
383C GLY
384C PRO
424C GLN
458C PHE
495C LYS
499C THR
500C ILE
501C GLU
503C 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
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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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
2ywb 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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XMP NAME: XANTHOSINE-5'-MONOPHOSPHATE
FORMULA: C10 H14 N4 O9 P1
SMILES: OC1C(O)C(OC1COP(O)(O)=O)[n]2c[nH+]c3C(=O)NC(=O)Nc23
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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