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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1fwl
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF HOMOSERINE KINASE TITLE
HOMOSERINE KINASE 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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16 ALA
17 ASN
22 PHE
23 ASP
34 ASP
50 VAL
54 ASN
55 ILE
56 PRO
61 LYS
62 ASN
63 VAL
64 ALA
85 ILE
87 LYS
90 LYS
91 ALA
92 GLY
93 SER
94 GLY
95 LEU
96 GLY
97 SER
98 SER
99 ALA
101 SER
130 GLU
133 SER
134 SER
138 HIS
140 ASP
141 ASN
181 ILE
182 ASN
183 THR
187 ARG
235 ARG
260 GLY
261 SER
262 GLY
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
1h74 ILEC_500 SAPD_400 _MGE_600 41 183 Details
ADPG_400 27 113
ADPB_400 27 109
ILEH_500 SAPI_400 40 174
1h72 ANPF1301 HSEG1300 39 166 Details
ANPB1301 HSEC1300 39 167
1h73 ANPB_418 THRA_401 38 154 Details
ANPD_418 THRC_401 38 152
1fwk ADPD_700 27 114 Details
ADPF_800 27 115
ADPB_600 27 115
ADPH_900 _MGI_597 28 120
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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