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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2c8m
LIGASE HEADER
STRUCTURE OF PROTEIN TA0514, PUTATIVE LIPOATE PROTEIN LIGASE FROM T. ACIDOPHILUM WITH BOUND LIPOIC ACID TITLE
LIPOATE-PROTEIN LIGASE A 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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LPA D 900
18D LEU
39D TYR
41D HIS
46D ILE
72D ARG
76D GLY
77D GLY
78D ALA
79D VAL
81D HIS
87D ASN
135D LYS
137D THR
138D ASP
145D LYS
148D GLY
149D ALA
150D ALA
161D HIS
162D ALA
163D ALA
LPA B 900
18B LEU
21B ASP
39B TYR
41B HIS
46B ILE
72B ARG
76B GLY
77B GLY
79B VAL
81B HIS
87B ASN
135B LYS
137B THR
138B ASP
145B LYS
148B GLY
149B ALA
150B ALA
161B HIS
162B ALA
163B ALA
LPA C 900
18C LEU
21C ASP
39C TYR
41C HIS
46C ILE
72C ARG
76C GLY
77C GLY
79C VAL
81C HIS
87C ASN
135C LYS
137C THR
138C ASP
145C LYS
148C GLY
149C ALA
150C ALA
161C HIS
162C ALA
163C ALA
LPA A 900
18A LEU
39A TYR
41A HIS
46A ILE
72A ARG
76A GLY
77A GLY
79A VAL
81A HIS
87A ASN
135A LYS
137A THR
138A ASP
145A LYS
148A GLY
149A ALA
150A ALA
161A HIS
162A ALA
163A 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
2c7i Details
other holo-structures
pdb ID Ligand Unique ID
2art AMPA_302 _MGA1301 LPAA_301 Details
2aru ATPA1065 _MGA1301 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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LPA NAME: LIPOIC ACID
FORMULA: C8 H14 O2 S2
SMILES: OC(=O)CCCCC1CCSS1
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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