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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2dto
LIGASE HEADER
CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM PYROCOCCUS HORIKOSHII OT3 COMPLEXED WITH ATP AND BIOTIN TITLE
235AA LONG HYPOTHETICAL BIOTIN--[ACETYL-COA- 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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BTN F1402
21D SER
22D THR
23D ASN
42D GLN
45D GLY
46D HIS
47D GLY
53D TRP
61D TRP
62D LEU
63D SER
103D ASN
104D ASP
111D LYS
114D GLY
115D VAL
116D LEU
127D GLY
128D ILE
129D GLY
BTN C1401
21A SER
22A THR
23A ASN
42A GLN
45A GLY
46A HIS
47A GLY
53A TRP
61A TRP
62A LEU
63A SER
103A ASN
104A ASP
111A LYS
114A GLY
115A VAL
116A LEU
127A GLY
128A ILE
129A GLY
ATP B1301
47A GLY
48A ARG
51A ARG
52A LYS
53A TRP
54A GLU
56A PRO
100A LYS
103A ASN
104A ASP
111A LYS
131A ASN
134A ASN
136A VAL
137A PRO
139A GLY
140A ALA
227A TYR
231A SER
232A LEU
233A ARG
ATP E1302
47D GLY
48D ARG
51D ARG
52D LYS
53D TRP
54D GLU
61D TRP
100D LYS
103D ASN
104D ASP
111D LYS
131D ASN
134D ASN
135D LYS
137D PRO
140D ALA
227D TYR
231D SER
232D LEU
233D 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
1wq7 Details
other holo-structures
pdb ID Ligand Unique ID
2dth BTNF1402 Details
BTNC1401
1x01 ATPE1002 Details
ATPB1001
2dkg BT5F1302 Details
BT5B1301 POPD4001 _MGC1001
2fyk ADPB1301 BTNC1401 Details
ADPE1302 BTNF1402
1wnl ADPE1302 Details
ADPB1301
1wqw BT5D1302 Details
BT5B1301
2dti BT5F1302 POPH1402 _MNG1502 Details
BT5B1301 POPD1401 _MNC1501
1wpy BTNB1301 Details
BTND1302
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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ATP NAME: ADENOSINE-5'-TRIPHOSPHATE
FORMULA: C10 H16 N5 O13 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C3O
BTN NAME: BIOTIN
FORMULA: C10 H16 N2 O3 S1
SMILES: OC(=O)CCCCC1SCC2NC(=O)NC12
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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