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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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1lx7 |
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STRUCTURE OF E. COLI URIDINE PHOSPHORYLASE AT 2.0A |
TITLE |
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URIDINE PHOSPHORYLASE |
COMPND |
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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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7 | |
PHE |
8 | |
HIS |
26 | |
GLY |
30 | |
ARG |
48 | |
ARG |
68 | |
GLY |
69 | |
ILE |
76 | |
ILE |
91 | |
ARG |
92 | |
ILE |
93 | |
GLY |
94 | |
THR |
95 | |
THR |
96 | |
GLY |
162 | |
PHE |
| 166 | |
GLN |
168 | |
ARG |
195 | |
TYR |
196 | |
GLU |
197 | |
MET |
198 | |
GLU |
220 | |
ILE |
221 | |
VAL |
223 | |
ARG |
229 | |
PRO |
1007 | |
PHE |
1008 | |
HIS |
1026 | |
GLY |
1030 | |
ARG |
1048 | |
ARG |
| 1068 | |
GLY |
1069 | |
ILE |
1076 | |
ILE |
1091 | |
ARG |
1092 | |
ILE |
1093 | |
GLY |
1094 | |
THR |
1095 | |
THR |
1096 | |
GLY |
1162 | |
PHE |
1166 | |
GLN |
1168 | |
ARG |
1195 | |
TYR |
1196 | |
GLU |
1197 | |
MET |
| 1198 | |
GLU |
1220 | |
ILE |
1221 | |
VAL |
1223 | |
ARG |
1229 | |
PRO |
2026 | |
GLY |
2027 | |
ASP |
2030 | |
ARG |
2069 | |
ILE |
2091 | |
ARG |
2092 | |
ILE |
2093 | |
GLY |
2094 | |
THR |
2095 | |
THR |
2096 | |
GLY |
| 2162 | |
PHE |
2166 | |
GLN |
2168 | |
ARG |
2195 | |
TYR |
2196 | |
GLU |
2197 | |
MET |
2198 | |
GLU |
2220 | |
ILE |
2221 | |
VAL |
2223 | |
ARG |
2229 | |
PRO |
3007 | |
PHE |
3008 | |
HIS |
3048 | |
ARG |
3076 | |
ILE |
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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 |
1rxu |
PO4K2101 THML2102 |
22 |
89 |
Details |
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PO4N2111 THMO2112 |
22 |
94 |
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PO4Q2121 THMR2122 |
22 |
86 |
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PO4H2091 THMI2092 |
22 |
95 |
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PO4E2081 THMF2082 |
22 |
91 |
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PO4B2071 THMC2072 |
22 |
96 |
1rxc |
R1PL2082 URFP2081 |
23 |
97 |
Details |
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R1PF2032 URFJ2031 |
23 |
85 |
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R1PD2012 URFB2011 |
23 |
83 |
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R1PI2002 URFG2001 |
23 |
84 |
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R1PO2022 URFM2021 |
23 |
88 |
3kvv |
R2BS_256 URFT_254 SO4R_255 |
23 |
89 |
Details |
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R2BG_256 URFH_254 SO4F_255 |
23 |
90 |
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R2BW_256 URFX_254 SO4V_255 |
23 |
94 |
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R2BC_256 SO4B_255 URFD_254 |
23 |
88 |
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R2BO_256 SO4N_255 URFP_254 |
23 |
92 |
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R2BK_256 URFL_254 SO4J_255 |
23 |
90 |
1rxs |
DURG2102 PO4F2101 |
21 |
94 |
Details |
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DURC3112 PO4B3111 |
21 |
82 |
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DURQ2112 PO4N2111 |
21 |
96 |
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DURL2122 PO4I2121 |
21 |
92 |
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v9.0 September 2010 |
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: 0.0742 seconds |