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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3crr
TRANSFERASE HEADER
STRUCTURE OF TRNA DIMETHYLALLYLTRANSFERASE: RNA MODIFICATION THROUGH A CHANNEL TITLE
TRNA DELTA(2)-ISOPENTENYLPYROPHOSPHATE 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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DPO A 326
14A THR
15A ALA
16A ALA
17A GLY
18A LYS
19A THR
37A ASP
50A ALA
101A GLY
102A GLY
223A ARG
288A GLN
TRS A 327
14A THR
37A ASP
39A ALA
48A GLY
49A THR
50A ALA
102A GLY
223A ARG
227A MET
254A ALA
255A VAL
281A THR
284A LEU
288A GLN
MG A 324
18A LYS
19A THR
40A LEU
50A ALA
52A PRO
CL A 325
37A ASP
40A LEU
49A THR
50A ALA
101A GLY
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
3crm Details
other holo-structures
pdb ID Ligand Unique ID
none
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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DPO NAME: DIPHOSPHATE
FORMULA: O7 P2
SMILES: [O-]P([O-])(=O)OP([O-])([O-])=O
TRS NAME: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
FORMULA: C4 H12 N1 O3
SMILES: [NH3+]C(CO)(CO)CO
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
CL NAME: CHLORIDE ION
FORMULA: CL1
SMILES: [Cl-]
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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