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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3pte
HYDROLASE, TRANSPEPTIDASE HEADER
THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6 A RESOLUTION TITLE
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE 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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61 GLY
62 SER
65 LYS
108 HIS
114 ASP
116 THR
117 ASN
120 PHE
121 ALA
123 THR
157 TYR
158 SER
159 TYR
161 ASN
164 PHE
214 LEU
217 ASP
233 TRP
234 ALA
237 ALA
238 GLY
274 VAL
275 ASN
277 THR
278 GLN
280 TYR
285 ARG
287 ARG
298 HIS
299 THR
300 GLY
301 THR
302 VAL
303 GLN
306 TYR
326 SER
327 ASN
328 ASN
329 VAL
332 LEU
333 ASN
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
1pwd CSCA_400 24 92 Details
1pw8 GOLA_500 H2AA_400 35 137 Details
1ceg CEPA_400 22 89 Details
1pwg HELA_400 29 125 Details
1iki DALA_500 REYA_400 27 131 Details
1hvb CEHA_401 51 157 Details
1cef CEFA_400 26 96 Details
1ikg REXA_400 26 117 Details
1mpl GOLA_500 RE1A_400 GOLA_501 33 142 Details
1scw CP5A_400 GOLA_500 GOLA_504 27 120 Details
1pw1 FORA_600 HELA_400 FORA_601 31 142 Details
1pwc PNMA_400 23 82 Details
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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