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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3hio
HYDROLASE/HYDROLASE INHIBITOR HEADER
CRYSTAL STRUCTURE OF RICIN A-CHAIN IN COMPLEX WITH THE CYCLIC TETRANUCLEOTIDE INHIBITOR, A TRANSITION STATE ANALOGUE TITLE
RICIN 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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C2X A 268
48A ARG
56A ARG
75A ASP
77A THR
78A ASN
79A ALA
80A TYR
81A VAL
82A VAL
93A PHE
94A HIS
95A PRO
96A ASP
97A ASN
100A ASP
104A ILE
120A GLY
121A GLY
122A ASN
123A TYR
124A ASP
172A ILE
176A SER
177A GLU
180A ARG
208A GLU
209A ASN
211A TRP
212A GLY
213A ARG
216A THR
230A ILE
256A VAL
258A ARG
C2X C 268
48C ARG
56C ARG
75C ASP
77C THR
78C ASN
79C ALA
80C TYR
81C VAL
82C VAL
93C PHE
94C HIS
95C PRO
96C ASP
97C ASN
100C ASP
104C ILE
120C GLY
121C GLY
122C ASN
123C TYR
124C ASP
172C ILE
176C SER
177C GLU
180C ARG
208C GLU
209C ASN
211C TRP
212C GLY
213C ARG
216C THR
230C ILE
256C VAL
258C ARG
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
1rtc Details
other holo-structures
pdb ID Ligand Unique ID
2p8n ADEA_271 SO4A_270 Details
1br6 PT1A_301 Details
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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C2X 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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