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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2dya
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF COMPLEX BETWEEN ADENINE NUCLEOTIDE AND NUCLEOSIDE DIPHOSPHATE KINASE 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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ADP C 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
125A ALA
ADP B 502
15Z LYS
55Z TYR
58Z HIS
61Z LYS
63Z PHE
67Z LEU
70Z TYR
91Z ARG
97Z THR
108Z ARG
117Z ASP
118Z ALA
119Z ILE
121Z ASN
124Z HIS
125Z ALA
ADP R 502
15P LYS
55P TYR
58P HIS
61P LYS
63P PHE
67P LEU
70P TYR
91P ARG
97P THR
108P ARG
117P ASP
118P ALA
119P ILE
121P ASN
124P HIS
125P ALA
ADP H 502
15F LYS
55F TYR
58F HIS
61F LYS
63F PHE
67F LEU
70F TYR
91F ARG
97F THR
108F ARG
117F ASP
118F ALA
119F ILE
121F ASN
124F HIS
125F ALA
ADP M 501
15K LYS
55K TYR
57K GLU
58K HIS
61K LYS
63K PHE
67K LEU
70K TYR
91K ARG
97K THR
108K ARG
117K ASP
118K ALA
119K ILE
121K ASN
124K HIS
125K ALA
ADP W 501
15U LYS
55U TYR
57U GLU
58U HIS
61U LYS
63U PHE
67U LEU
70U TYR
91U ARG
97U THR
108U ARG
117U ASP
118U ALA
119U ILE
121U ASN
124U HIS
125U ALA
MG E 601
55A TYR
57A GLU
58A HIS
91A ARG
124A HIS
125A ALA
127A ASP
MG D 602
55Z TYR
57Z GLU
58Z HIS
91Z ARG
124Z HIS
127Z ASP
MG T 602
55P TYR
57P GLU
58P HIS
91P ARG
124P HIS
125P ALA
127P ASP
MG J 602
55F TYR
57F GLU
58F HIS
91F ARG
124F HIS
125F ALA
127F ASP
MG O 601
55K TYR
57K GLU
58K HIS
91K ARG
124K HIS
125K ALA
127K ASP
MG Y 601
55U TYR
57U GLU
58U HIS
91U ARG
124U HIS
125U ALA
127U 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
Help

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
2dxf GNPR_501 Details
GNPD_501
GNPK_501
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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ADP NAME: ADENOSINE-5'-DIPHOSPHATE
FORMULA: C10 H15 N5 O10 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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