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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2hvd
SIGNALING PROTEIN,TRANSFERASE HEADER
HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A COMPLEXED WITH ADP TITLE
NUCLEOSIDE DIPHOSPHATE KINASE A 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 H 160
12G LYS
52G TYR
55G LEU
58G ARG
60G PHE
64G LEU
67G TYR
88G ARG
94G THR
105G ARG
112G VAL
113G GLY
115G ASN
118G HIS
119G GLY
121G ASP
152A GLU
ADP D 160
12C LYS
52C TYR
55C LEU
60C PHE
64C LEU
67C TYR
88C ARG
94C THR
105C ARG
112C VAL
113C GLY
115C ASN
118C HIS
119C GLY
121C ASP
152E GLU
ADP F 160
12E LYS
52E TYR
55E LEU
58E ARG
60E PHE
64E LEU
67E TYR
88E ARG
94E THR
105E ARG
112E VAL
113E GLY
115E ASN
118E HIS
119E GLY
121E ASP
152K GLU
ADP L 160
12K LYS
52K TYR
55K LEU
58K ARG
60K PHE
64K LEU
67K TYR
88K ARG
94K THR
105K ARG
112K VAL
113K GLY
115K ASN
118K HIS
119K GLY
121K ASP
152C GLU
ADP J 160
12I LYS
52I TYR
55I LEU
58I ARG
60I PHE
64I LEU
67I TYR
88I ARG
94I THR
105I ARG
112I VAL
113I GLY
115I ASN
118I HIS
119I GLY
121I ASP
152G GLU
ADP B 160
12A LYS
52A TYR
55A LEU
60A PHE
64A LEU
67A TYR
88A ARG
94A THR
105A ARG
112A VAL
113A GLY
115A ASN
118A HIS
119A GLY
121A ASP
152I 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:

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
1jxv Details
other holo-structures
pdb ID Ligand Unique ID
none
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
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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