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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1wfc
TRANSFERASE HEADER
STRUCTURE OF APO, UNPHOSPHORYLATED, P38 MITOGEN ACTIVATED PROTEIN KINASE P38 (P38 MAP KINASE) THE MAMMALIAN HOMOLOGUE OF THE YEAST HOG1 PROTEIN TITLE
MITOGEN-ACTIVATED PROTEIN KINASE P38 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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29 PRO
30 VAL
31 GLY
32 SER
33 GLY
34 ALA
35 TYR
38 VAL
51 ALA
52 VAL
53 LYS
71 GLU
74 LEU
75 LEU
84 ILE
85 GLY
86 LEU
104 LEU
105 VAL
106 THR
107 HIS
108 LEU
109 MET
110 GLY
111 ALA
112 ASP
115 ASN
154 SER
155 ASN
156 LEU
157 ALA
167 LEU
168 ASP
169 PHE
170 GLY
171 LEU
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
3gfe P37A_361 33 123 Details
3itz P66A_401 31 136 Details
3fc1 52PX_362 28 104 Details
3zya 2A8A_400 24 120 Details
1m7q DQOA_501 33 134 Details
3ds6 A17A_361 30 163 Details
A17B_361 30 168
1ouy 094A_501 34 143 Details
3lhj LHJA_361 32 127 Details
1ouk 084A_501 37 140 Details
1yqj 6NPA_362 35 140 Details
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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