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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1aux
SYNAPSE HEADER
STRUCTURE OF THE C DOMAIN OF SYNAPSIN IA FROM BOVINE BRAIN WITH CALCIUM ATP-GAMMA-S BOUND TITLE
SYNAPSIN IA 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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SAP E 800
225D LYS
247D ILE
267D VAL
269D LYS
274D HIS
275D SER
276D GLY
279D LYS
305D GLU
306D PRO
307D PHE
308D ILE
310D ALA
313D ASP
328D ARG
373D GLU
375D LEU
385D ILE
386D GLU
SAP H 800
225G LYS
247G ILE
267G VAL
269G LYS
274G HIS
275G SER
276G GLY
279G LYS
305G GLU
306G PRO
307G PHE
308G ILE
310G ALA
313G ASP
328G ARG
373G GLU
375G LEU
385G ILE
386G GLU
393G PRO
CA I 801
225G LYS
373G GLU
386G GLU
388G VAL
SAP K 800
225J LYS
247J ILE
267J VAL
269J LYS
274J HIS
275J SER
276J GLY
279J LYS
305J GLU
306J PRO
307J PHE
308J ILE
310J ALA
313J ASP
328J ARG
373J GLU
375J LEU
385J ILE
386J GLU
393J PRO
CA L 801
225J LYS
373J GLU
386J GLU
388J VAL
SAP B 800
225A LYS
247A ILE
267A VAL
269A LYS
274A HIS
275A SER
276A GLY
279A LYS
305A GLU
306A PRO
307A PHE
308A ILE
310A ALA
313A ASP
328A ARG
373A GLU
375A LEU
385A ILE
386A GLU
388A VAL
CA F 801
373D GLU
386D GLU
388D VAL
CA C 801
373A GLU
386A GLU
388A 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
1auv 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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SAP NAME: ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
FORMULA: C10 H16 N5 O12 P3 S1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=S)C(O)C3O
CA NAME: CALCIUM ION
FORMULA: CA1
SMILES: [Ca++]
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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