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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3ng5
TRANSPORT PROTEIN HEADER
CRYSTAL STRUCTURE OF V30M TRANSTHYRETIN COMPLEXED WITH (-)- EPIGALLOCATECHIN GALLATE (EGCG) TITLE
TRANSTHYRETIN 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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KDH D 128
18D ASP
20D VAL
21D ARG
23D SER
78D TYR
79D TRP
82D LEU
83D GLY
84C ILE
85C SER
113D PRO
114C TYR
KDH A 128
18A ASP
20A VAL
21A ARG
23A SER
78A TYR
79A TRP
82A LEU
83A GLY
84F ILE
85F SER
113A PRO
114F TYR
KDH F 128
31F HIS
32F VAL
33F PHE
40F THR
41F TRP
42F GLU
43F PRO
44F PHE
45F ALA
46F SER
72F GLU
90F HIS
KDH A 129
31A HIS
32A VAL
33A PHE
40A THR
41A TRP
42A GLU
43A PRO
44A PHE
45A ALA
46A SER
72A GLU
90A HIS
KDH C 128
31C HIS
32C VAL
33C PHE
40C THR
41C TRP
42C GLU
43C PRO
44C PHE
45C ALA
46C SER
72C GLU
90C HIS
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
3djt Details
other holo-structures
pdb ID Ligand Unique ID
3kgt GEND3071 GENH3071 Details
GENB3071 GENF3071
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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KDH 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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