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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1wkj
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM THERMUS THERMOPHILUS HB8 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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7 MET
9 LYS
48 HIS
49 TYR
51 GLU
52 HIS
55 LYS
56 PRO
57 PHE
60 GLY
61 LEU
64 PHE
85 ARG
88 MET
91 THR
92 HIS
94 LYS
102 ARG
109 ILE
110 ASP
112 ASN
114 ILE
115 HIS
116 GLY
118 ALA
126 GLU
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
1wkk GDPN1001 28 101 Details
GDPK1001 28 97
GDPH1001 28 104
GDPQ1001 28 101
GDPB1001 28 101
GDPE1001 28 97
1wkl ADPB_646 PHSC_138 31 107 Details
ADPH_646 PHSI_138 31 105
ATPW_856 _MGX_900 32 122
ADPT_646 PHSU_138 31 107
ADPF_646 PHSG_138 31 104
ATPQ_856 _MGR_900 32 123
ADPN_646 PHSO_138 31 109
ADPZ_646 PHSA_138 31 110
ATPC_856 _MGD_900 32 121
ATPK_856 _MGL_900 32 123
ATPE_856 _MGF_900 32 119
ATPI_856 _MGJ_900 32 120
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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