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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3fux
TRANSFERASE HEADER
T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121 TITLE
DIMETHYLADENOSINE TRANSFERASE 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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MTA C 272
25C PHE
26C GLY
27C GLN
28C ASN
29C PHE
53C VAL
54C GLY
56C GLY
74C ILE
75C GLU
76C LYS
77C ASP
80C LEU
98C GLN
99C ASP
100C ALA
101C LEU
117C ASN
118C LEU
119C PRO
120C TYR
121C HIS
122C ILE
184C PHE
MTA B 272
25B PHE
26B GLY
27B GLN
28B ASN
29B PHE
53B VAL
54B GLY
56B GLY
74B ILE
75B GLU
76B LYS
77B ASP
80B LEU
98B GLN
99B ASP
100B ALA
101B LEU
117B ASN
118B LEU
119B PRO
120B TYR
121B HIS
122B ILE
184B PHE
MTA A 272
25A PHE
26A GLY
27A GLN
28A ASN
29A PHE
53A VAL
54A GLY
56A GLY
74A ILE
75A GLU
76A LYS
77A ASP
80A LEU
98A GLN
99A ASP
100A ALA
101A LEU
117A ASN
118A LEU
119A PRO
120A TYR
121A HIS
122A ILE
184A PHE
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).

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apo-structure
pdb ID
3fut Details
other holo-structures
pdb ID Ligand Unique ID
3fuw MTAA_272 Details
3fuu ADNA___0 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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MTA NAME: 5'-DEOXY-5'-METHYLTHIOADENOSINE
FORMULA: C11 H15 N5 O3 S1
SMILES: CSCC1OC(C(O)C1O)[n]2cnc3c(N)ncnc23
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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