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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3dws
OXIDOREDUCTASE HEADER
LEISHMANIA MAJOR COPROPORPHYRINOGEN III OXIDASE WITH BOUND LIGAND TITLE
COPROPORPHYRINOGEN III OXIDASE 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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FIC A 303
78A ARG
93A SER
107A HIS
109A ASN
111A ARG
171A TYR
187A PHE
189A ASP
249A ASP
250A ARG
251A GLY
254A PHE
FIC C 304
78C ARG
93C SER
107C HIS
109C ASN
111C ARG
171C TYR
172C PHE
187C PHE
189C ASP
249C ASP
250C ARG
251C GLY
254C PHE
ACT B 302
93A SER
95A VAL
107A HIS
172A PHE
181A ARG
241A TYR
245A ASN
249A ASP
252A THR
265A ILE
267A ILE
268A SER
ACT D 302
93C SER
95C VAL
107C HIS
172C PHE
181C ARG
241C TYR
245C ASN
249C ASP
252C THR
265C ILE
267C ILE
268C SER
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
1vju Details
other holo-structures
pdb ID Ligand Unique ID
3dwr 0PAF_504 0PAF_505 0PAF_506 ACTG_401 Details
0PAA_501 0PAA_503 0PAA_502 ACTB_402
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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ACT NAME: ACETATE ION
FORMULA: C2 H3 O2
SMILES: CC([O-])=O
FIC NAME: not_found
FORMULA: not_found
SMILES: not_found
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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