university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1qid
HYDROLASE HEADER
SPECIFIC CHEMICAL AND STRUCTURAL DAMAGE AT NINE TIME POINTS (POINT A) CAUSED BY INTENSE SYNCHROTRON RADIATION TO TORPEDO CALIFORNICA ACETYLCHOLINESTERASE TITLE
ACETYLCHOLINESTERASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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4 SER
5 GLU
7 LEU
8 VAL
9 ASN
10 THR
11 LYS
70 TYR
72 ASP
73 GLU
74 GLN
81 SER
84 TRP
105 ARG
106 PRO
107 LYS
116 TYR
117 GLY
118 GLY
119 GLY
121 TYR
122 SER
123 GLY
127 LEU
130 TYR
185 GLN
186 PHE
188 GLY
199 GLU
200 SER
201 ALA
233 TRP
279 TRP
280 ASN
282 LEU
284 PHE
285 ASP
286 SER
287 ILE
288 PHE
289 ARG
290 PHE
330 PHE
331 PHE
334 TYR
335 GLY
400 VAL
432 TRP
439 ILE
440 HIS
441 GLY
442 TYR
444 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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
2c4h ACEM1543 AT3O1540 13 79 Details
ACEF1543 AT3H1540 13 81
2vt7 PGEN1539 PGEO1540 20 127 Details
2wg1 MESA2541 PG4A2547 PG4A2546 38 114 Details
FP1A2540 _GBA2539 14 85
1qti GNTD_600 21 90 Details
GNTB_600 21 98
1vot HUPB_999 18 82 Details
HUPD_999 18 85
2vjb CCDI1539 10 72 Details
CCDP1539 10 73
2ack EDRD_999 12 75 Details
EDRB_999 12 74
1amn NAFF_594 17 87 Details
NAFC_594 17 87
2wg0 PEGK2549 PG4J2542 _GBI2540 24 123 Details
PEGN2549 _GBL2540 PG4M2542 24 124
1gpn HUBC1538 19 85 Details
HUBG1538 19 86
2vjc CCDJ1537 10 71 Details
1gpk HUPF1540 18 80 Details
HUPL1540 18 84
1oce MF2D_700 19 100 Details
MF2B_700 19 103
2xi4 PGES1004 10 79 Details
AFTL1000 23 94
AFTA1000 23 102
1ax9 EDRD_999 12 78 Details
EDRB_999 12 71
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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