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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1i7l
NEUROPEPTIDE HEADER
CRYSTAL STRUCTURE ANALYSIS OF THE COMPLEX OF THE C DOMAIN OF SYNAPSIN II FROM RAT WITH ATP TITLE
SYNAPSIN II 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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ATP H 801
189G HIS
226G LYS
248G ILE
268G VAL
270G LYS
275G HIS
276G SER
277G GLY
280G LYS
306G GLU
307G PRO
308G PHE
309G ILE
311G ALA
314G ASP
329G ARG
336G TRP
337G LYS
338G THR
339G ASN
374G LYS
376G VAL
386G PHE
387G GLU
389G MET
ATP D 801
189C HIS
226C LYS
248C ILE
268C VAL
270C LYS
275C HIS
276C SER
277C GLY
280C LYS
306C GLU
307C PRO
308C PHE
309C ILE
311C ALA
314C ASP
329C ARG
336C TRP
337C LYS
338C THR
339C ASN
374C LYS
376C VAL
386C PHE
387C GLU
389C MET
ATP F 800
226E LYS
248E ILE
268E VAL
270E LYS
275E HIS
276E SER
277E GLY
280E LYS
306E GLU
307E PRO
308E PHE
309E ILE
311E ALA
314E ASP
329E ARG
336E TRP
337E LYS
338E THR
339E ASN
374E LYS
376E VAL
386E PHE
387E GLU
389E MET
394E PRO
396E ILE
ATP B 800
226A LYS
248A ILE
268A VAL
270A LYS
276A SER
277A GLY
280A LYS
306A GLU
307A PRO
308A PHE
309A ILE
311A ALA
314A ASP
329A ARG
336A TRP
337A LYS
338A THR
339A ASN
374A LYS
376A VAL
386A PHE
387A GLU
389A MET
394A PRO
396A ILE
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
1i7n 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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ATP NAME: ADENOSINE-5'-TRIPHOSPHATE
FORMULA: C10 H16 N5 O13 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)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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