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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1tyf
PEPTIDASE HEADER
THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS TITLE
CLP PEPTIDASE 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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34 GLN
66 PRO
67 GLY
68 GLY
69 VAL
70 ILE
71 THR
94 GLN
96 ALA
97 SER
98 MET
101 PHE
118 ARG
119 VAL
120 MET
121 ILE
122 HIS
123 GLN
124 PRO
125 LEU
126 GLY
127 GLY
129 GLN
138 HIS
141 GLU
142 ILE
145 VAL
146 LYS
149 MET
150 ASN
153 MET
168 THR
173 PHE
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
2fzs CMQK_507 31 147 Details
CMQO_505 31 139
CMQA_504 31 136
CMQY_514 31 132
CMQG_502 GOLX3005 37 167
CMQV_513 GOLS3011 37 172
CMQB_501 GOLC3002 37 163
CMQG_509 GOLH3008 37 163
CMQK_510 31 136
CMQV_503 GOLW3006 37 156
CMQR_512 GOLO3010 37 168
CMQD_508 GOLZ3007 37 166
CMQR_506 GOLL3009 37 168
CMQN_511 31 131
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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