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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1ygj
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF PYRIDOXAL KINASE IN COMPLEX WITH ROSCOVITINE AND DERIVATIVES TITLE
PYRIDOXAL 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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RMC D1001
12C SER
14C VAL
19C VAL
20C GLY
41C VAL
43C PHE
45C ASN
46C HIS
47C THR
48C GLY
52C TRP
56C VAL
84C TYR
86C ARG
115C VAL
127C TYR
231C VAL
232C GLY
234C GLY
235C ASP
RMC B1001
12A SER
14A VAL
19A VAL
20A GLY
41A VAL
43A PHE
45A ASN
46A HIS
47A THR
48A GLY
52A TRP
56A VAL
84A TYR
86A ARG
115A VAL
127A TYR
231A VAL
232A GLY
234A GLY
235A 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
1lhp Details
other holo-structures
pdb ID Ligand Unique ID
1yhj R6CD_313 Details
R6CB_313
1rfu ADPD2402 _ZNB2403 PLPC2401 Details
ADPH7402 PLPG7401 _ZNF7403
1rft ACPH_401 _ZNG_403 __KI_404 Details
ACPC_401 _ZNB_403 __KD_404
1ygk RRCD1001 Details
RRCB1001
1rfv ADPF1401 _ZNE1402 Details
ADPC_401 _ZNB_402
1lhr ATPG_402 _ZNF_404 __KH_406 Details
ATPC_401 _ZNB_403 __KD_405
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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RMC NAME: (2R)-2-({6-[BENZYL(METHYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)BUTAN-1-OL
FORMULA: C20 H28 N6 O1
SMILES: CCC(CO)Nc1nc(N(C)Cc2ccccc2)c3nc[n](C(C)C)c3n1
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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