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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2i4m
LIGASE HEADER
RHODOPSEUDOMONAS PALUSTRIS PROLYL-TRNA SYNTHETASE IN COMPLEX WITH PROAMS TITLE
PROLINE-TRNA LIGASE 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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PSD D 439
109C THR
111C GLU
140C ARG
142C GLU
149C VAL
150C MET
151C ARG
152C GLY
155C PHE
157C MET
159C ASP
161C TYR
282C GLU
283C VAL
284C GLY
285C GLN
287C PHE
315C SER
316C TYR
317C GLY
319C GLY
322C ARG
PSD B 439
109A THR
111A GLU
140A ARG
142A GLU
149A VAL
150A MET
151A ARG
152A GLY
155A PHE
157A MET
159A ASP
161A TYR
282A GLU
283A VAL
284A GLY
285A GLN
287A PHE
315A SER
316A TYR
317A GLY
319A GLY
322A 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
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
2i4l Details
other holo-structures
pdb ID Ligand Unique ID
2i4n 5CAD_439 Details
5CAB_439
2i4o ATPC_441 _MGB_439 _MGD_440 Details
ATPG_441 _MGF_439 _MGH_440
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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PSD NAME: 5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE
FORMULA: C15 H22 N7 O7 P1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)NC(=O)C4CCCN4)C(O)C3O
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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