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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2e1t
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF DENDRANTHEMA MORIFOLIUM DMAT COMPLEXED WITH MALONYL-COA TITLE
ACYL 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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MLC B1001
36A TRP
42A ILE
170A HIS
174A ASP
175A ALA
176A SER
178A ARG
260A LYS
264A LEU
270A LEU
271A GLU
272A TYR
273A VAL
274A SER
275A SER
276A PHE
277A THR
300A PHE
301A PRO
302A ILE
303A ASP
307A ARG
321A VAL
350A LEU
351A HIS
383A TRP
384A VAL
385A SER
386A GLY
387A THR
388A PRO
389A LYS
390A LEU
426A GLU
MLC D1002
36C TRP
42C ILE
170C HIS
174C ASP
175C ALA
176C SER
178C ARG
260C LYS
270C LEU
271C GLU
272C TYR
273C VAL
274C SER
275C SER
276C PHE
300C PHE
301C PRO
302C ILE
303C ASP
307C ARG
321C VAL
350C LEU
351C HIS
383C TRP
384C VAL
385C SER
386C GLY
387C THR
388C PRO
389C LYS
390C LEU
426C GLU
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
2e1u 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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MLC NAME: MALONYL-COENZYME A
FORMULA: C24 H38 N7 O19 P3 S1
SMILES: CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)[n]2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCSC(=O)CC(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
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