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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1zdf
TRANSFERASE HEADER
SER162 MUTANT OF GLYCOGENIN COMPLEXED WITH UDP-GLUCOSE AND MANGANESE TITLE
GLYCOGENIN-1 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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UPG B 411
8A LEU
9A THR
10A THR
11A ASN
14A TYR
81A VAL
85A LYS
99A PHE
101A ASP
102A ALA
103A ASP
124A ASP
132A ASN
133A SER
134A GLY
159A ASP
161A GLY
162A SER
163A GLN
196E TYR
211A HIS
213A LEU
214A GLY
217A LYS
UPG F 411
8E LEU
9E THR
10E THR
11E ASN
14E TYR
81E VAL
85E LYS
99E PHE
101E ASP
102E ALA
103E ASP
124E ASP
132E ASN
133E SER
134E GLY
159E ASP
161E GLY
162E SER
163E GLN
196A TYR
211E HIS
213E LEU
214E GLY
217E LYS
MN C 400
101A ASP
103A ASP
211A HIS
MN G 400
101E ASP
103E ASP
211E HIS
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
1zcu 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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UPG NAME: URIDINE-5'-DIPHOSPHATE-GLUCOSE
FORMULA: C15 H24 N2 O17 P2
SMILES: OCC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N3C=CC(=O)NC3=O)C(O)C(O)C1O
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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