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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1n43
BIOTIN-BINDING PROTEIN HEADER
STREPTAVIDIN MUTANT N23A WITH BIOTIN AT 1.89A TITLE
STREPTAVIDIN 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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BTN B5400
23G ALA
25G LEU
27G SER
43G TYR
45G SER
47G VAL
48G GLY
49G ASN
50G ALA
79G TRP
86G ALA
88G SER
90G THR
92G TRP
108G TRP
110G LEU
112G SER
120A TRP
128G ASP
BTN H5100
23A ALA
25A LEU
27A SER
43A TYR
45A SER
47A VAL
48A GLY
49A ASN
50A ALA
79A TRP
86A ALA
88A SER
90A THR
92A TRP
108A TRP
110A LEU
112A SER
120G TRP
128A ASP
BTN D5300
23E ALA
25E LEU
27E SER
43E TYR
45E SER
47E VAL
48E GLY
49E ASN
50E ALA
79E TRP
86E ALA
88E SER
90E THR
92E TRP
108E TRP
110E LEU
112E SER
120C TRP
128E ASP
BTN F5200
23C ALA
25C LEU
27C SER
43C TYR
45C SER
47C VAL
48C GLY
49C ASN
50C ALA
79C TRP
86C ALA
88C SER
90C THR
92C TRP
108C TRP
110C LEU
112C SER
120E TRP
128C ASP
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
1n4j 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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BTN NAME: BIOTIN
FORMULA: C10 H16 N2 O3 S1
SMILES: OC(=O)CCCCC1SCC2NC(=O)NC12
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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