university lille north of france LigASite database of binding sites
Home
News
Introduction
Methods
Flow Chart
References
Download
About
FAQ
Search
LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
(click to remove window)
Browse dataset
holo-structureHelp

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

(click anywhere in this window to remove it)
3i0g
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF GTB C80S/C196S + DA + UDP-GAL TITLE
ABO GLYCOSYLTRANSFERASE 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 C 357
72A PRO
74A PRO
75A LYS
78A THR
79A PRO
80A SER
85H LEU
87H VAL
89H PRO
97A GLU
98A GLY
99A THR
100A PHE
101A ASN
102A ILE
UDP J 357
72H PRO
74H PRO
75H LYS
78H THR
79H PRO
80H SER
85A LEU
87A VAL
89A PRO
97H GLU
98H GLY
99H THR
100H PHE
101H ASN
102H ILE
UDP I 358
121H PHE
122H ALA
123H ILE
124H LYS
126H TYR
188H ARG
210H VAL
211H ASP
212H VAL
213H ASP
266H MET
268H ALA
UDP B 358
121A PHE
122A ALA
123A ILE
124A LYS
126A TYR
188A ARG
210A VAL
211A ASP
212A VAL
213A ASP
266A MET
268A ALA
GAL M 359
188H ARG
266H MET
267H GLY
300H TRP
301H HIS
302H ASP
303H GLU
GAL F 359
188A ARG
266A MET
267A GLY
268A ALA
300A TRP
301A HIS
302A ASP
303A GLU
MN K 2
211H ASP
213H ASP
214H MET
266H MET
268H ALA
MN D 2
211A ASP
213A ASP
214A MET
266A MET
268A ALA
BHG L 1
233H HIS
235H SER
236H PHE
245H THR
264H TYR
266H MET
300H TRP
303H GLU
329H LEU
FUC N 356
233H HIS
234H PRO
235H SER
266H MET
326H ASP
329H LEU
330H LEU
343H ALA
BHG E 1
233A HIS
235A SER
236A PHE
245A THR
264A TYR
266A MET
300A TRP
303A GLU
329A LEU
FUC G 356
233A HIS
234A PRO
235A SER
266A MET
326A ASP
329A LEU
330A LEU
343A ALA
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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)
» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
3i0c Details
other holo-structures
pdb ID Ligand Unique ID
3i0d UDPD___1 Details
UDPB___1
3i0f __UA___1 Details
BHGI_400 UDPG_357 _MNH___2 FUCJ_356
BHGD_400 UDPB_357 FUCE_356 _MNC___2
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++]
BHG NAME: 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
FORMULA: C12 H24 O6
SMILES: CCCCCCOC1OC(CO)C(O)C(O)C1O
FUC NAME: FUCOSE
FORMULA: C6 H12 O5
SMILES: CC1OC(O)C(O)C(O)C1O
GAL NAME: D-GALACTOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)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
Script execution time: 0.2472 seconds