university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

(click anywhere in this window to remove it)
3g2p
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF THE GLYCOPEPTIDE N-METHYLTRANSFERASE MTFA COMPLEXED WITH (S)-ADENOSYL-L-HOMOCYSTEINE (SAH) TITLE
PCZA361.24 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
SAH A 500
69A GLU
70A LEU
71A ALA
72A ALA
73A GLY
74A MET
76A ARG
77A LEU
91A LEU
92A GLU
93A LEU
94A SER
97A VAL
121A GLY
122A ASP
123A MET
124A SER
138A SER
140A GLY
141A SER
144A GLU
145A LEU
SAH B 500
71B ALA
73B GLY
91B LEU
92B GLU
93B LEU
94B SER
97B VAL
121B GLY
122B ASP
123B MET
124B SER
138B SER
140B GLY
141B SER
144B GLU
145B LEU
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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
3g2m Details
other holo-structures
pdb ID Ligand Unique ID
3g2q SFGB_500 Details
SFGC_400
SFGD_500
SFGA_400
3g2o SAMB_600 Details
SAMA_500
SAMC_500
SAMD_600
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.

(click anywhere in this window to remove it)
SAH NAME: S-ADENOSYL-L-HOMOCYSTEINE
FORMULA: C14 H20 N6 O5 S1
SMILES: NC(CCSCC1OC(C(O)C1O)[n]2cnc3c(N)ncnc23)C(O)=O
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
Script execution time: 0.1092 seconds