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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2xi4
HYDROLASE HEADER
TORPEDO CALIFORNICA ACETYLCHOLINESTERASE IN COMPLEX WITH AFL B1 (ORTHORHOMBIC SPACE GROUP) TITLE
ACETYLCHOLINESTERASE 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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AFT L1000
70L TYR
72L ASP
121L TYR
279L TRP
282L LEU
284L PHE
286L SER
287L ILE
288L PHE
289L ARG
290L PHE
330L PHE
331L PHE
334L TYR
335L GLY
AFT A1000
70A TYR
72A ASP
121A TYR
279A TRP
282A LEU
284A PHE
285A ASP
286A SER
287A ILE
288A PHE
289A ARG
290A PHE
330A PHE
331A PHE
334A TYR
335A GLY
PGE S1004
84L TRP
117L GLY
118L GLY
119L GLY
121L TYR
122L SER
130L TYR
199L GLU
200L SER
290L PHE
330L PHE
331L PHE
440L HIS
441L GLY
442L TYR
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1qid Details
other holo-structures
pdb ID Ligand Unique ID
2c4h ACEM1543 AT3O1540 Details
ACEF1543 AT3H1540
2vt7 PGEN1539 PGEO1540 Details
2wg1 MESA2541 PG4A2547 PG4A2546 Details
FP1A2540 _GBA2539
1qti GNTD_600 Details
GNTB_600
1vot HUPB_999 Details
HUPD_999
2vjb CCDI1539 Details
CCDP1539
2ack EDRD_999 Details
EDRB_999
1amn NAFF_594 Details
NAFC_594
2wg0 PEGK2549 PG4J2542 _GBI2540 Details
PEGN2549 _GBL2540 PG4M2542
1gpn HUBC1538 Details
HUBG1538
2vjc CCDJ1537 Details
1gpk HUPF1540 Details
HUPL1540
1oce MF2D_700 Details
MF2B_700
1ax9 EDRD_999 Details
EDRB_999
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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PGE NAME: TRIETHYLENE GLYCOL
FORMULA: C6 H14 O4
SMILES: OCCOCCOCCO
AFT NAME: not_found
FORMULA: not_found
SMILES: not_found
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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