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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1ybu
HYDROLASE HEADER
MYCOBACTERIUM TUBERCULOSIS ADENYLYL CYCLASE RV1900C CHD, IN COMPLEX WITH A SUBSTRATE ANALOG. TITLE
LIPJ 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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APC D 602
300C PHE
302D ASP
304D VAL
305D GLY
306D SER
307D THR
308D GLN
341C VAL
343C THR
344D ALA
345D GLY
346D ASP
349C VAL
377D ARG
395C ASP
396C VAL
401C VAL
402C HIS
405C ALA
406C ARG
442C LYS
APC A 601
300B PHE
302A ASP
304A VAL
305A GLY
306A SER
307A THR
308A GLN
341B VAL
343B THR
344A ALA
345A GLY
346A ASP
349B VAL
377A ARG
395B ASP
396B VAL
401B VAL
402B HIS
405B ALA
406B ARG
442B LYS
MN D 502
302D ASP
303D ILE
306D SER
346D ASP
MN A 501
302A ASP
303A ILE
306A SER
346A 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
1ybt 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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APC NAME: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
FORMULA: C11 H18 N5 O12 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)CP(O)(=O)OP(O)(O)=O)C(O)C3O
MN NAME: MANGANESE (II) ION
FORMULA: MN1
SMILES: [Mn++]
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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