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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2x6o
TRANSCRIPTION HEADER
TET REPRESSOR CLASS D IN COMPLEX WITH 7-CHLOR-2-CYANO-ISO-TETRACYCLINE TITLE
TETRACYCLINE REPRESSOR PROTEIN CLASS D 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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2TC A1209
60A LEU
64A HIS
67A SER
79A LEU
82A ASN
83A ALA
86A PHE
100A HIS
105A PRO
109A GLN
110A TYR
112A THR
113A VAL
116A GLN
131A LEU
134A ILE
135A SER
137A VAL
138A SER
139A HIS
147D GLU
170D LEU
174D LEU
177D MET
2TC D1209
60D LEU
64D HIS
67D SER
78D PHE
79D LEU
82D ASN
83D ALA
86D PHE
100D HIS
105D PRO
109D GLN
110D TYR
112D THR
113D VAL
116D GLN
131D LEU
134D ILE
135D SER
137D VAL
138D SER
139D HIS
147A GLU
170A LEU
174A LEU
177A MET
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
1bjz Details
other holo-structures
pdb ID Ligand Unique ID
1bjy CTCD_222 _MGE_223 Details
CTCB_222
2x9d ITCA1209 Details
ITCF1209
1ork ATCC_222 _MGB_223 Details
ATCF_222 _MGE_223
2fj1 CTCH_222 _NIJ_223 Details
CTCC_222 _NIE_223
2xpt TDCE1209 __KF1210 Details
TDCK1209 __KL1210
2xps TDCF_222 _MGE_223 Details
TDCL_222 _MGK_223
2xpw OTCE_222 _MGF_223 Details
OTCL_222 _MGM_223
2vke TACF_222 _COD_223 Details
TACL_222 _COJ_223
2xpv MIYK1209 _MGJ1210 Details
MIYV1209 _MGU1210
2xpu TDCD1209 Details
TDCH1209
1bj0 CTCD_222 Details
CTCB_222
2o7o DXTD_222 _MGE_223 Details
DXTI_222 _MGJ_223
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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2TC NAME: not_found
FORMULA: not_found
SMILES: not_found
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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