university lille north of france LigASite database of binding sites
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LigASite v3.0 (nr25) - non-redundant
LigASite v3.0 (redundant) - redundant
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apo-structureHelp

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

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1lhp
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF PYRIDOXAL KINASE FROM SHEEP BRAIN TITLE
PYRIDOXAL 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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12 SER
14 VAL
19 VAL
20 GLY
40 SER
41 VAL
43 PHE
45 ASN
46 HIS
47 THR
48 GLY
52 TRP
56 VAL
84 TYR
85 THR
86 ARG
113 ASP
115 VAL
118 ASP
119 GLN
120 ARG
127 TYR
148 THR
149 PRO
150 ASN
153 GLU
186 THR
187 SER
199 LEU
201 ALA
223 MET
224 HIS
225 LYS
226 VAL
228 ALA
230 PHE
231 VAL
232 GLY
233 THR
234 GLY
235 ASP
237 PHE
260 VAL
263 MET
264 HIS
267 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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
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
1ygk RRCD1001 26 124 Details
RRCC1001 26 120
1rfv ADPC_401 ZN2C_402 28 122 Details
ADPC1401 ZN2C1402 28 118
1yhj R6CD___1 26 127 Details
R6CC___1 26 124
1rfu ADPE4402 ZN2E4403 PLPE4401 43 176 Details
ADPA_402 ZN2A_403 PLPA_401 43 181
1rft ACPC_401 ZN2C_403 __KC_404 33 137 Details
ACPD_401 ZN2D_403 __KD_404 33 139
1lhr ATPC_402 _ZNC_404 __KC_406 33 143 Details
ATPC_401 _ZNC_403 __KC_405 33 131
1ygj RMCC1001 27 110 Details
RMCD1001 27 113
v3.0
January 2008		 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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