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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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| 1tyv |
| VIRAL ADHESION PROTEIN |
HEADER |
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| STRUCTURE OF TAILSPIKE-PROTEIN |
TITLE |
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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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| 178 | |
ASN |
| 235 | |
THR |
| 236 | |
VAL |
| 237 | |
SER |
| 240 | |
VAL |
| 257 | |
ASN |
| 283 | |
LEU |
| 285 | |
ARG |
| 302 | |
LYS |
| 303 | |
ASP |
| 304 | |
GLY |
| 307 | |
THR |
| 309 | |
GLU |
| 311 | |
LEU |
| 331 | |
VAL |
| | 332 | |
SER |
| 335 | |
GLN |
| 337 | |
LEU |
| 359 | |
GLU |
| 360 | |
SER |
| 363 | |
LYS |
| 365 | |
TRP |
| 366 | |
GLN |
| 369 | |
VAL |
| 370 | |
GLY |
| 391 | |
TRP |
| 392 | |
ASP |
| 395 | |
ASP |
| 400 | |
THR |
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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 |
| 1tyu |
GALB___1 TYVB___3 MANB___6 TYVB___7 RAMB___8 GALB___5 RAMB___4 MANB___2 |
83 |
173 |
Details |
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GALC___1 TYVC___3 GALC___5 MANC___2 MANC___6 RAMC___4 TYVC___7 RAMC___8 |
83 |
170 |
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GALA___1 TYVA___7 RAMA___8 GALA___5 MANA___6 TYVA___3 RAMA___4 MANA___2 |
83 |
167 |
| 1tyw |
GALC___1 MANC___2 GLCC___9 TYVC___3 MANC___6 RAMC___4 GALC___5 TYVC___7 RAMC___8 |
94 |
204 |
Details |
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GALB___1 RAMB___8 GALB___5 RAMB___4 GLCB___9 TYVB___3 MANB___6 TYVB___7 MANB___2 |
94 |
202 |
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GALA___1 TYVA___7 MANA___2 RAMA___8 GALA___5 MANA___6 GLCA___9 TYVA___3 RAMA___4 |
94 |
203 |
| 1tyx |
ABEC___3 GALC___5 MANC___2 MANC___6 RAMC___4 RAMC___8 ABEC___7 GALC___1 |
83 |
159 |
Details |
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ABEA___3 RAMA___8 GALA___5 MANA___6 RAMA___4 GALA___1 ABEA___7 MANA___2 |
83 |
160 |
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ABEB___3 MANB___6 ABEB___7 RAMB___8 GALB___1 GALB___5 RAMB___4 MANB___2 |
83 |
158 |
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v3.0
January 2008 |
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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