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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1gqt
TRANSFERASE HEADER
ACTIVATION OF RIBOKINASE BY MONOVALENT CATIONS TITLE
RIBOKINASE 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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RIB D1311
14A ASN
16A ASP
30E THR
41A GLY
42A GLY
43A LYS
46A ASN
98A ALA
100A ILE
110A ILE
112A ILE
143A GLU
251A ILE
252A ALA
255A ASP
291A ALA
ACP G1310
43E LYS
166E ASN
187E ASN
190E GLU
223E THR
225E GLY
226E SER
228E GLY
242E GLY
243E PHE
244E ARG
245E VAL
247E ALA
250E THR
251E ILE
252E ALA
253E ALA
254E GLY
255E ASP
257E PHE
279E HIS
282E ALA
283E ALA
286E VAL
ACP C1310
43A LYS
166A ASN
168A ALA
187A ASN
188A GLU
190A GLU
223A THR
225A GLY
226A SER
228A GLY
242A GLY
243A PHE
244A ARG
245A VAL
247A ALA
250A THR
251A ILE
252A ALA
253A ALA
254A GLY
255A ASP
257A PHE
279A HIS
282A ALA
283A ALA
286A VAL
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
1rka Details
other holo-structures
pdb ID Ligand Unique ID
1rk2 ADPC_310 Details
ADPH_310
1rkd ADPF_310 Details
ADPB_310
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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ACP NAME: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FORMULA: C11 H18 N5 O12 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)CP(O)(O)=O)C(O)C3O
RIB NAME: RIBOSE
FORMULA: C5 H10 O5
SMILES: OCC1OC(O)C(O)C1O
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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