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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2dg3
ISOMERASE HEADER
WILDTYPE FK506-BINDING PROTEIN COMPLEXED WITH RAPAMYCIN TITLE
FK506-BINDING PROTEIN 1A 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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RAP A 501
26A TYR
36A PHE
37A ASP
42A ARG
46A PHE
47A LYS
48A PHE
53A GLN
54A GLU
55A VAL
56A ILE
59A TRP
82A TYR
87A HIS
90A ILE
91A ILE
99A 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:

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
2ppn Details
other holo-structures
pdb ID Ligand Unique ID
1f40 GPIA_108 Details
1nsg RADA_108 Details
1qpl 587A_108 Details
587C_308
1qpf 858D_108 B7GG_109 858J_308 858E_308 B7GB_109 858I_108 Details
B7GG_109 858E_308 858I_108
1fkb RAPA_108 Details
1a7x FKAB_201 Details
3fap ARDA_402 Details
2fap RADA_108 Details
1j4h SUBA_201 Details
1fkh SBXA_108 Details
2fke FK5F_108 FK5D_108 FK5H_108 Details
FK5B_108 FK5F_108 FK5D_108 FK5H_108
1j4i TSTA_201 Details
1fkd 818B_108 818D_108 Details
818F_108 818H_108
1fkg SB3A_108 Details
1fap RAPA_108 Details
1fkf FK5B_108 FK5F_108 FK5D_108 FK5H_108 Details
1fki SB1B_108 Details
SB1A_109
1j4r 001B_109 Details
001A_108
001D_109
4fap ARDA_402 Details
1fkj FK5B_108 FK5F_108 FK5D_108 FK5H_108 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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RAP NAME: RAPAMYCIN IMMUNOSUPPRESSANT DRUG
FORMULA: C51 H79 N1 O13
SMILES: COC1CC(CCC1O)CC(C)C2CC(=O)C(C)C=C(C)C(O)C(OC)C(=O)C(C)CC(C)C=CC=CC=C(C)C(CC3CCC(C)C(O)(O3)C(=O)C(=O)N4CCCCC4C(=O)O2)OC
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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