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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1zxy
TRANSFERASE HEADER
ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH PRPP AND MAGNESIUM TITLE
ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE 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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PRP B 348
77A THR
78A ALA
79A GLY
81A GLY
82A GLY
83A ASP
84A GLY
86A GLY
87A THR
88A VAL
89A ASN
90A VAL
91A SER
92A THR
106A LYS
107A HIS
108A GLY
109A ASN
116A SER
118A SER
191A GLY
222A ILE
223A ASP
224A GLU
PRP F 348
77E THR
78E ALA
79E GLY
81E GLY
82E GLY
83E ASP
86E GLY
87E THR
88E VAL
89E ASN
90E VAL
91E SER
92E THR
106E LYS
107E HIS
108E GLY
109E ASN
116E SER
118E SER
191E GLY
222E ILE
223E ASP
224E GLU
MG C 346
79A GLY
91A SER
MG G 346
79E GLY
MG D 347
223A ASP
224A GLU
MG H 347
223E ASP
224E 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
1o17 Details
other holo-structures
pdb ID Ligand Unique ID
2gvq BE2D_601 BE2E_602 Details
1zyk BE2J_804 _MGI_706 PRPG_603 BE2K_801 _MGH_705 Details
PRPB_602 _MGC_703 _MGD_704
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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PRP NAME: ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
FORMULA: C5 H13 O14 P3
SMILES: OC1C(O)C(OC1COP(O)(O)=O)OP(O)(=O)OP(O)(O)=O
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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