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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2ihz
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF MULTIFUNCTIONAL SIALYLTRANSFERASE FROM PASTEURELLA MULTOCIDA WITH CMP-3F-NEU5AC AND ALPHA-LACTOSE BOUND TITLE
ALPHA-2,3/2,6-SIALYLTRANSFERASE/SIALIDASE 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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LBT A3824
34A PRO
35A ALA
63A ARG
85A ASN
112A HIS
141A ASP
144A MET
270A TRP
313A ARG
CSF A1741
35A ALA
36A SER
37A LEU
40A LEU
63A ARG
141A ASP
142A GLY
143A SER
144A MET
147A VAL
265A THR
266A GLY
267A THR
268A THR
269A THR
270A TRP
280A TYR
309A LYS
310A GLY
311A HIS
312A PRO
335A ILE
336A SER
337A PHE
338A GLU
354A ALA
355A SER
356A SER
357A LEU
372A THR
388A TYR
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
2ex0 Details
other holo-structures
pdb ID Ligand Unique ID
2ihk CSFA1741 Details
2ihj CSFA1741 Details
2iiq C5PB1427 Details
C5PA1427
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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CSF NAME: CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID
FORMULA: C20 H30 N4 O16 F1 P1
SMILES: CC(=O)NC1C(O)C(F)C(OC1C(O)C(O)CO)(OP(O)(=O)OCC2OC(C(O)C2O)N3C=CC(=NC3=O)N)C(O)=O
LBT NAME: LACTOSE
FORMULA: C12 H22 O11
SMILES: OCC1OC(OC2C(O)C(O)C(O)OC2CO)C(O)C(O)C1O
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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