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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1uak
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF TRNA(M1G37)METHYLTRANSFERASE: INSIGHT INTO TRNA RECOGNITION TITLE
TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE 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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SAM A 301
86A TYR
87A LEU
88A SER
89A PRO
90A GLN
113A GLY
114A ARG
115A TYR
116A GLU
117A GLY
131A TRP
132A SER
133A ILE
134A GLY
136A TYR
137A VAL
138A LEU
139A THR
140A GLY
141A GLY
144A PRO
154B ARG
170B SER
177B ASP
178B CYS
180B HIS
SAM B 301
86B TYR
87B LEU
88B SER
89B PRO
90B GLN
113B GLY
114B ARG
115B TYR
116B GLU
117B GLY
131B TRP
132B SER
133B ILE
134B GLY
136B TYR
137B VAL
138B LEU
139B THR
140B GLY
141B GLY
144B PRO
154A ARG
170A SER
177A ASP
178A CYS
180A 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
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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
1uaj Details
other holo-structures
pdb ID Ligand Unique ID
1ual SAHA_301 Details
SAHB_301
1uam SAHA_301 Details
SAHC_301
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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SAM NAME: S-ADENOSYLMETHIONINE
FORMULA: C15 H22 N6 O5 S1
SMILES: C[S+](CCC(N)C([O-])=O)CC1OC(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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