university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

(click anywhere in this window to remove it)
1nvk
TRANSFERASE HEADER
T4 PHAGE BGT IN COMPLEX WITH UDP AND A MN2+ ION AT 1.8 A RESOLUTION TITLE
DNA BETA-GLUCOSYLTRANSFERASE 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
UDP A 700
18A VAL
22A GLU
100A ASP
186A TYR
187A GLY
188A GLY
189A SER
191A ARG
195A ARG
213A PHE
214A GLY
237A LYS
238A ILE
240A MET
243A VAL
256A ILE
261A TYR
267A THR
268A LEU
269A ARG
272A GLU
MN A 701
22A GLU
99A THR
100A ASP
163A GLU
261A TYR
267A THR
268A LEU
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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
2bgt Details
other holo-structures
pdb ID Ligand Unique ID
1j39 UPGA_400 Details
1c3j UDPA_353 Details
1jiu UDPA_353 _MGA_354 Details
1m5r TRSE_501 UDPB_401 Details
1jix UDPA_500 _CAA_600 Details
1jg7 UDPA_400 _MNA_401 Details
2bgu UDPA_353 Details
1ixy UDPB_401 _MGD_501 Details
1qkj UDPA_353 Details
1jg6 UDPA_400 Details
1jiv UDPA_353 _MGA_354 Details
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.

(click anywhere in this window to remove it)
UDP NAME: URIDINE-5'-DIPHOSPHATE
FORMULA: C9 H14 N2 O12 P2
SMILES: OC1C(O)C(OC1COP(O)(=O)OP(O)(O)=O)N2C=CC(=O)NC2=O
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
Script execution time: 0.1922 seconds