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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3lts
LYASE HEADER
CRYSTAL STRUCTURE OF THE MUTANT V182A,I199A OF OROTIDINE 5'- MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUT COMPLEXED WITH INHIBITOR BMP TITLE
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE 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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BMP D 229
18C ALA
20C ASP
42C LYS
70C ASP
72C LYS
75A ASP
76A ILE
79A THR
96C ILE
123C LEU
125C GLU
126C MET
127C SER
155C VAL
156C GLY
157C PRO
180C PRO
181C GLY
182C ALA
184C ALA
185C GLN
200C ILE
201C VAL
202C GLY
203C ARG
204C SER
206C TYR
BMP B 229
18A ALA
20A ASP
42A LYS
70A ASP
72A LYS
75C ASP
76C ILE
79C THR
96A ILE
123A LEU
125A GLU
126A MET
127A SER
155A VAL
156A GLY
157A PRO
180A PRO
181A GLY
182A ALA
184A ALA
185A GLN
200A ILE
201A VAL
202A GLY
203A ARG
204A SER
206A TYR
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
3m5x 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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BMP NAME: 6-HYDROXYURIDINE-5'-PHOSPHATE
FORMULA: C9 H13 N2 O10 P1
SMILES: OC1C(O)C(OC1COP(O)(O)=O)N2C(=O)NC(=O)C=C2O
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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