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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1qpf
ISOMERASE HEADER
FK506 BINDING PROTEIN (12 KDA, HUMAN) COMPLEX WITH L-709,858 TITLE
PROTEIN (FK506-BINDING PROTEIN) 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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858 J 308
21F THR
46F PHE
47F LYS
48F PHE
49F MET
52F LYS
54F GLU
85A THR
86A GLY
87A HIS
88A PRO
90A ILE
226C TYR
236C PHE
237C ASP
242C ARG
246C PHE
254C GLU
255C VAL
256C ILE
259C TRP
281C ALA
282C TYR
287C HIS
290C ILE
291C ILE
299C PHE
858 E 308
21A THR
46A PHE
47A LYS
48A PHE
49A MET
52A LYS
54A GLU
85F THR
86F GLY
87F HIS
88F PRO
90F ILE
226H TYR
236H PHE
237H ASP
242H ARG
246H PHE
254H GLU
255H VAL
256H ILE
259H TRP
281H ALA
282H TYR
287H HIS
290H ILE
291H ILE
299H PHE
858 D 108
26A TYR
36A PHE
37A ASP
42A ARG
46A PHE
54A GLU
55A VAL
56A ILE
59A TRP
81A ALA
82A TYR
88F PRO
89F GLY
90A ILE
91A ILE
99A PHE
284C ALA
285C THR
287H HIS
288H PRO
858 I 108
26F TYR
36F PHE
37F ASP
42F ARG
46F PHE
54F GLU
55F VAL
56F ILE
59F TRP
81F ALA
82F TYR
88A PRO
89A GLY
90A ILE
91F ILE
99F PHE
284H ALA
285H THR
287C HIS
288C PRO
B7G G 109
82F TYR
85F THR
87F HIS
90F ILE
91F ILE
282H TYR
283H GLY
284H ALA
285H THR
B7G B 109
82A TYR
85A THR
87A HIS
90A ILE
91A ILE
282C TYR
283C GLY
284C ALA
285C THR
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
2ppn Details
other holo-structures
pdb ID Ligand Unique ID
2dg3 RAPA_501 Details
1f40 GPIA_108 Details
1nsg RADA_108 Details
1qpl 587A_108 Details
587C_308
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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858 NAME: C32-O-(1-ETHYL-INDOL-5-YL)ASCOMYCIN
FORMULA: C53 H78 N2 O12
SMILES: CCC1C=C(C)CC(C)CC(OC)C2OC(O)(C(C)CC2OC)C(=O)C(=O)N3CCCCC3C(=O)OC(C(C)C(O)CC1=O)C(C)=CC4CCC(Oc5ccc6[n](CC)ccc6c5)C(C4)OC
B7G NAME: HEPTYL-BETA-D-GLUCOPYRANOSIDE
FORMULA: C13 H26 O6
SMILES: CCCCCCCOC1OC(CO)C(O)C(O)C1O
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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