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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1ddt
TOXIN HEADER
THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION TITLE
DIPHTHERIA TOXIN 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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APU B 950
20A TYR
21A HIS
22A GLY
23A THR
24A LYS
27A TYR
30A SER
31A ILE
34A GLY
35A ILE
36A GLN
38A PRO
42A THR
43A GLN
44A GLY
52A GLY
53A PHE
54A TYR
55A SER
56A THR
62A ALA
65A TYR
69A ASN
148A GLU
153A TRP
446C SER
458C ARG
APU D 950
20C TYR
21C HIS
22C GLY
23C THR
24C LYS
27C TYR
30C SER
31C ILE
34C GLY
35C ILE
36C GLN
38C PRO
42C THR
43C GLN
44C GLY
52C GLY
53C PHE
54C TYR
55C SER
56C THR
62C ALA
65C TYR
69C ASN
148C GLU
153C TRP
446A SER
458A 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
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
1sgk Details
other holo-structures
pdb ID Ligand Unique ID
1tox NADB_536 Details
NADD_536
1f0l APUA_601 _CLA_704 Details
APUB_602 _CLB_709
1mdt APUB_901 Details
APUA_901
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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APU NAME: ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE
FORMULA: C19 H25 N7 O15 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(CO)C(OP(O)(=O)OCC4OC(C(O)C4OP(O)(O)=O)N5C=CC(=O)NC5=O)C3O
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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