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LigASite database of binding sites |
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PDB ID and HEADER , TITLE and
COMPND records of the PDB file. | (click anywhere in this window to remove it) |
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1ul9 |
SUGAR BINDING PROTEIN |
HEADER |
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Figure highlighting the binding site residues. Figures were drawn with
Molscript (7) and rendered with
Raster3D (8). PISA coordinates
(3) are used when available
(all entries except NMR). | (click anywhere in this window to remove it) |
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List of binding site residues detected in this protein. Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand. Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type. Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein. | (click anywhere in this window to remove it) |
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36 | |
THR |
38 | |
VAL |
40 | |
ASN |
51 | |
HIS |
53 | |
SER |
55 | |
ARG |
58 | |
GLU |
62 | |
VAL |
64 | |
ASN |
66 | |
ARG |
72 | |
TRP |
75 | |
GLU |
77 | |
ARG |
126 | |
ASN |
127 | |
ALA |
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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) |
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Links to external databases: |
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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) |
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Table describing the holo-structures and ligands used to define
the binding sites.
Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand;
a space-separated list of HET -groups that constitute
the ligand (see Methods).
Each HET -group in the ligand is uniquely identified by
a string in which the first four characters are the three-letter
HET ID from the PDB file followed by the chain ID from
the PISA file, and the last four characters are the residue sequence
number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic
contacts. | (click anywhere in this window to remove it) |
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pdb ID |
Ligand Unique ID |
#atoms |
#contacts |
1ulf |
A2GD_151 BGCC_153 FUCE_154 GALB_152 |
47 |
86 |
Details |
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A2GN_151 BGCM_153 FUCO_154 GALL_152 |
47 |
87 |
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A2GI_151 FUCJ_154 GALG_152 BGCH_153 |
47 |
86 |
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A2GS_151 BGCR_153 FUCT_154 GALQ_152 |
47 |
87 |
1ule |
GALJ_152 GLAK_151 NAGL_153 |
37 |
73 |
Details |
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GALF_152 NAGH_153 GLAG_151 |
37 |
71 |
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GALN_152 GLAO_151 NAGP_153 |
37 |
74 |
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GALB_152 NAGD_153 GLAC_151 |
37 |
70 |
1uld |
FUCP_153 NAGO_152 GALN_151 |
36 |
70 |
Details |
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FUCL_153 GALJ_151 NAGK_152 |
36 |
71 |
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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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