university lille north of france LigASite database of binding sites
holo-structureHelp

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

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2dxf
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE IN COMPLEX WITH GTP ANALOG TITLE
NUCLEOSIDE DIPHOSPHATE KINASE COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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GNP R 501
15O LYS
55O TYR
57O GLU
58O HIS
61O LYS
63O PHE
67O LEU
70O TYR
91O ARG
97O THR
108O ARG
117O ASP
118O ALA
119O ILE
121O ASN
124O HIS
127O ASP
GNP D 501
15A LYS
55A TYR
57A GLU
58A HIS
61A LYS
63A PHE
67A LEU
70A TYR
91A ARG
97A THR
108A ARG
117A ASP
118A ALA
119A ILE
121A ASN
124A HIS
127A ASP
GNP K 501
15H LYS
55H TYR
57H GLU
58H HIS
61H LYS
63H PHE
67H LEU
70H TYR
91H ARG
97H THR
108H ARG
117H ASP
118H ALA
119H ILE
121H ASN
124H HIS
127H 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:

LigPlot (hosted at the EBI):

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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Hide table of related structures
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List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
2cwk Details
other holo-structures
pdb ID Ligand Unique ID
2dxd ANPF_502 Details
ANPX_502
ANPR_502
ANPL_502
ANPG_501 ANPI_501
ANPA_501 ANPC_501
ANPJ_502
ANPO_501 ANPU_501
ANPD_502
2dya ADPC_501 _MGE_601 Details
ADPB_502 _MGD_602
ADPR_502 _MGT_602
ADPH_502 _MGJ_602
ADPM_501 _MGO_601
ADPW_501 _MGY_601
2dy9 ADPK_501 _MGM_601 Details
ADPC_501 _MGE_601
ADPS_501 _MGU_601
2dxe GDPK_501 _MGM_601 Details
GDPC_501 _MGE_601
GDPS_501 _MGU_601
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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GNP NAME: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
FORMULA: C10 H17 N6 O13 P3
SMILES: NC1=Nc2[n](cnc2C(=O)N1)C3OC(COP(O)(=O)OP(O)(=O)NP(O)(O)=O)C(O)C3O
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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