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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2cwk
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF NUCLEOTIDE DIPHOSPHATE KINASE FROM PYROCOCCUS HORIKOSHII TITLE
NUCLEOSIDE-DIPHOSPHATE 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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15 LYS
55 TYR
57 GLU
58 HIS
61 LYS
62 PRO
63 PHE
67 LEU
70 TYR
85 TYR
91 ARG
97 THR
100 LYS
108 ARG
117 ASP
118 ALA
119 ILE
121 ASN
124 HIS
125 ALA
127 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
2dxd ANPF_502 23 88 Details
ANPX_502 23 88
ANPR_502 23 88
ANPL_502 23 91
ANPG_501 ANPI_501 46 189
ANPA_501 ANPC_501 46 189
ANPJ_502 23 88
ANPO_501 ANPU_501 46 194
ANPD_502 23 91
2dya ADPC_501 _MGE_601 28 100 Details
ADPB_502 _MGD_602 28 95
ADPR_502 _MGT_602 28 97
ADPH_502 _MGJ_602 28 93
ADPM_501 _MGO_601 28 100
ADPW_501 _MGY_601 28 94
2dxf GNPR_501 24 89 Details
GNPD_501 24 89
GNPK_501 24 90
2dy9 ADPK_501 _MGM_601 28 93 Details
ADPC_501 _MGE_601 28 97
ADPS_501 _MGU_601 28 94
2dxe GDPK_501 _MGM_601 29 107 Details
GDPC_501 _MGE_601 29 104
GDPS_501 _MGU_601 29 103
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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