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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2deq
LIGASE HEADER
CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH BIOTINYL-5'-AMP, K111G MUTATION 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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BT5 D1302
21C SER
22C THR
23C ASN
42C GLN
45C GLY
46C HIS
47C GLY
48C ARG
51C ARG
52C LYS
53C TRP
54C GLU
61C TRP
62C LEU
63C SER
103C ASN
104C ASP
111C GLY
114C GLY
115C VAL
116C LEU
127C GLY
128C ILE
129C GLY
131C ASN
134C ASN
137C PRO
140C ALA
BT5 B1301
21A SER
22A THR
23A ASN
42A GLN
45A GLY
46A HIS
47A GLY
48A ARG
51A ARG
52A LYS
53A TRP
54A GLU
56A PRO
61A TRP
62A LEU
63A SER
103A ASN
104A ASP
111A GLY
112A ILE
114A GLY
115A VAL
116A LEU
127A GLY
128A ILE
129A GLY
131A ASN
134A ASN
137A PRO
140A ALA
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
2e1h Details
other holo-structures
pdb ID Ligand Unique ID
none
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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BT5 NAME: BIOTINYL-5-AMP
FORMULA: C20 H28 N7 O9 P1 S1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OC(=O)CCCCC4SCC5NC(=O)NC45)C(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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