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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1rid
IMMUNE SYSTEM HEADER
VACCINIA COMPLEMENT PROTEIN IN COMPLEX WITH HEPARIN TITLE
COMPLEMENT CONTROL PROTEIN 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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IDS A 247
13B PHE
15B ASN
214A LYS
215A CYS
217A TYR
218A GLY
219A TYR
221A LEU
SGN A 246
13B PHE
34B LEU
35B CYS
36B LEU
37B PRO
213A PHE
214A LYS
221A LEU
SGN A 248
15B ASN
16B SER
19B THR
218A GLY
219A TYR
220A LYS
IDS A 249
19B THR
20B ASP
217A TYR
218A GLY
220A LYS
244A ARG
SGN A 252
20B ASP
21B ALA
22B ASN
SGN A 250
21B ALA
216A LYS
217A TYR
218A GLY
219A TYR
244A ARG
IDS A 245
35B CYS
36B LEU
37B PRO
IDS B 247
214B LYS
215B CYS
217B TYR
218B GLY
219B TYR
SGN B 250
216B LYS
217B TYR
218B GLY
219B TYR
244B ARG
IDS B 249
217B TYR
218B GLY
244B ARG
SGN B 248
217B TYR
218B GLY
219B TYR
220B LYS
IDS A 251
244A ARG
IDS B 251
244B ARG
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
1g40 Details
other holo-structures
pdb ID Ligand Unique ID
1y8e SVRB_502 Details
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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IDS NAME: O2-SULFO-GLUCURONIC ACID
FORMULA: C6 H10 O10 S1
SMILES: OC1OC(C(O)C(O)C1OS(O)(=O)=O)C(O)=O
SGN NAME: N,O6-DISULFO-GLUCOSAMINE
FORMULA: C6 H13 N1 O11 S2
SMILES: OC1OC(COS(O)(=O)=O)C(O)C(O)C1NS(O)(=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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