university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1swc
BIOTIN-BINDING PROTEIN HEADER
APO-CORE-STREPTAVIDIN AT PH 4.5 TITLE
STREPTAVIDIN COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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23 ASN
25 LEU
27 SER
43 TYR
45 SER
47 VAL
48 GLY
49 ASN
50 ALA
54 TYR
79 TRP
84 ARG
86 ALA
88 SER
90 THR
92 TRP
108 TRP
110 LEU
112 SER
120 TRP
121 LYS
124 LEU
127 HIS
128 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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
3ry1 MRDF4001 MRDG4006 16 75 Details
1swd BTNF_300 16 76 Details
BTNB_600 16 80
2gh7 BTNR5200 16 79 Details
BTNE5100 16 81
BTNI5200 16 74
BTNN5100 16 78
2f01 BTNR5200 16 78 Details
BTNE5100 16 78
BTNI5200 16 74
BTNN5100 16 76
1swe BTND_500 16 81 Details
BTNB_600 16 76
BTNH_300 16 82
BTNF_400 16 78
1mk5 BTNH5100 16 80 Details
BTND5100 16 77
BTNJ5200 16 80
BTNB5200 16 76
BTNL5100 16 80
BTNP5100 16 77
BTNN5200 16 76
BTNF5200 16 80
3ry2 BTNG5001 16 76 Details
BTNU5001 16 79
BTNC5001 GOLM4003 22 97
BTNJ5001 GOLF4003 22 97
BTNX5001 GOLT4003 22 97
BTNQ5001 GOLA4003 22 97
BTNN5001 16 79
BTNB5001 16 76
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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