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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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1hqk |
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CRYSTAL STRUCTURE ANALYSIS OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS |
TITLE |
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6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE |
COMPND |
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The XML file of this protein (apo PDB ID 1hqk) is larger than 10MB. Clicking on any of the "Details" links for the holo-structures will start processing this file to show all HETgroup/Residue contacts. The entire process may take between 10 seconds and 1 minute, depending on server load; be patient while the page loads and do not click "Details" multiple times. |
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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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20 | |
SER |
22 | |
PHE |
23 | |
ASN |
54 | |
PRO |
55 | |
GLY |
56 | |
SER |
57 | |
TRP |
58 | |
GLU |
80 | |
VAL |
81 | |
LEU |
82 | |
ILE |
84 | |
GLY |
85 | |
ALA |
86 | |
THR |
88 | |
HIS |
| 89 | |
PHE |
92 | |
ILE |
112 | |
THR |
113 | |
PHE |
127 | |
ARG |
131 | |
LYS |
132 | |
HIS |
135 | |
LYS |
138 | |
GLU |
139 | |
ALA |
142 | |
SER |
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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 |
1nqw |
5YLF3201 |
27 |
117 |
Details |
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5YLC1201 |
27 |
111 |
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5YLI1201 |
27 |
116 |
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5YL94201 |
27 |
117 |
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5YLG5201 |
27 |
113 |
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5YLG2201 |
27 |
117 |
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5YLA6201 |
27 |
118 |
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5YLD3201 |
27 |
115 |
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5YL92201 |
27 |
119 |
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5YLI4201 |
27 |
119 |
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5YLH1201 |
27 |
110 |
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5YLJ3201 |
27 |
117 |
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5YL82201 |
27 |
114 |
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5YLC2201 |
27 |
113 |
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5YLI2201 |
27 |
117 |
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5YLE4201 |
27 |
113 |
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5YL84201 |
27 |
116 |
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5YL85201 |
27 |
118 |
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5YL95201 |
27 |
113 |
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5YLH4201 |
27 |
115 |
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5YLA5201 |
27 |
113 |
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5YLJ1201 |
27 |
115 |
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5YLB3201 |
27 |
108 |
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5YLF2201 |
27 |
112 |
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5YLD1201 |
27 |
116 |
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5YLB2201 |
27 |
119 |
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5YL83201 |
27 |
119 |
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5YLH2201 |
27 |
112 |
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5YLH5201 |
27 |
111 |
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5YLE1201 |
27 |
115 |
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5YLF5201 |
27 |
111 |
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5YLE3201 |
27 |
113 |
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5YLB4201 |
27 |
117 |
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5YLH3201 |
27 |
117 |
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5YLJ4201 |
27 |
120 |
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5YLB5201 |
27 |
113 |
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5YLD5201 |
27 |
113 |
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5YLI5201 |
27 |
113 |
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5YLC5201 |
27 |
118 |
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5YLF1201 |
27 |
110 |
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5YLE2201 |
27 |
114 |
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5YLI3201 |
27 |
115 |
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5YLC4201 |
27 |
115 |
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5YLJ5201 |
27 |
113 |
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5YLA4201 |
27 |
114 |
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5YLE5201 |
27 |
118 |
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5YLJ2201 |
27 |
117 |
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5YLG1201 |
27 |
115 |
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5YLF4201 |
27 |
115 |
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5YLG3201 |
27 |
117 |
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5YLD4201 |
27 |
119 |
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5YL81201 |
27 |
111 |
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5YLD2201 |
27 |
117 |
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5YLG4201 |
27 |
120 |
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5YL93201 |
27 |
108 |
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5YLB1201 |
27 |
115 |
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5YLA3201 |
27 |
114 |
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5YLA2201 |
27 |
115 |
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5YL91201 |
27 |
115 |
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5YLC3201 |
27 |
119 |
1nqv |
LMZ92201 |
20 |
91 |
Details |
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LMZG2201 |
20 |
89 |
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LMZ82201 |
20 |
87 |
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LMZG1201 |
20 |
85 |
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LMZD4201 |
20 |
85 |
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LMZB5201 |
20 |
91 |
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LMZB3201 |
20 |
89 |
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LMZA3201 |
20 |
88 |
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LMZF4201 |
20 |
90 |
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LMZI3201 |
20 |
91 |
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LMZ85201 |
20 |
90 |
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LMZH1201 |
20 |
88 |
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LMZD5201 |
20 |
89 |
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LMZJ3201 |
20 |
92 |
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LMZE4201 |
20 |
87 |
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LMZE1201 |
20 |
88 |
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LMZC3201 |
20 |
90 |
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LMZI2201 |
20 |
85 |
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LMZ93201 |
20 |
89 |
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LMZA2201 |
20 |
88 |
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LMZG4201 |
20 |
90 |
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LMZG3201 |
20 |
92 |
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LMZE3201 |
20 |
91 |
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LMZC4201 |
20 |
87 |
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LMZD3201 |
20 |
91 |
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LMZJ4201 |
20 |
90 |
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LMZ94201 |
20 |
88 |
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LMZE2201 |
20 |
88 |
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LMZH5201 |
20 |
91 |
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LMZD2201 |
20 |
85 |
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LMZB1201 |
20 |
90 |
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LMZJ2201 |
20 |
89 |
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LMZI4201 |
20 |
85 |
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LMZ95201 |
20 |
91 |
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LMZA5201 |
20 |
87 |
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LMZJ5201 |
20 |
91 |
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LMZI5201 |
20 |
89 |
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LMZA6201 |
20 |
90 |
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LMZD1201 |
20 |
88 |
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LMZ83201 |
20 |
90 |
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LMZA4201 |
20 |
91 |
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LMZH3201 |
20 |
88 |
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LMZ84201 |
20 |
87 |
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LMZG5201 |
20 |
91 |
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LMZB4201 |
20 |
88 |
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LMZH2201 |
20 |
89 |
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LMZC5201 |
20 |
90 |
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LMZF1201 |
20 |
88 |
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LMZC2201 |
20 |
87 |
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LMZ91201 |
20 |
90 |
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LMZF5201 |
20 |
91 |
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LMZF2201 |
20 |
89 |
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LMZJ1201 |
20 |
85 |
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LMZC1201 |
20 |
90 |
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LMZF3201 |
20 |
88 |
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LMZ81201 |
20 |
90 |
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LMZB2201 |
20 |
91 |
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LMZI1201 |
20 |
88 |
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LMZH4201 |
20 |
90 |
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LMZE5201 |
20 |
90 |
1nqx |
PO4F2251 RLPF2201 |
32 |
131 |
Details |
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PO4C3251 RLPC3201 |
32 |
127 |
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PO484251 RLP84201 |
32 |
131 |
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PO4C2251 RLPC2201 |
32 |
129 |
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PO4E3251 RLPE3201 |
32 |
135 |
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PO4H2251 RLPH2201 |
32 |
137 |
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PO491251 RLP91201 |
32 |
132 |
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PO4D5251 RLPD5201 |
32 |
130 |
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PO4D3251 RLPD3201 |
32 |
130 |
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PO4F3251 RLPF3201 |
32 |
135 |
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PO4C4251 RLPC4201 |
32 |
129 |
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PO4A6251 RLPA6201 |
32 |
134 |
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PO4B2251 RLPB2201 |
32 |
131 |
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PO4D4251 RLPD4201 |
32 |
131 |
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PO4G4251 RLPG4201 |
32 |
129 |
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PO4E2251 RLPE2201 |
32 |
139 |
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PO4B5251 RLPB5201 |
32 |
131 |
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PO493251 RLP93201 |
32 |
127 |
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PO495251 RLP95201 |
32 |
133 |
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PO4G3251 RLPG3201 |
32 |
131 |
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PO4F5251 RLPF5201 |
32 |
134 |
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PO4F4251 RLPF4201 |
32 |
131 |
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PO4A5251 RLPA5201 |
32 |
131 |
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PO4J3251 RLPJ3201 |
32 |
134 |
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PO4H5251 RLPH5201 |
32 |
136 |
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PO482251 RLP82201 |
32 |
133 |
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PO4B4251 RLPB4201 |
32 |
127 |
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PO4A3251 RLPA3201 |
32 |
131 |
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PO4H4251 RLPH4201 |
32 |
129 |
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PO4D1251 RLPD1201 |
32 |
132 |
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PO485251 RLP85201 |
32 |
130 |
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PO4J1251 RLPJ1201 |
32 |
133 |
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PO4I5251 RLPI5201 |
32 |
131 |
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PO4I2251 RLPI2201 |
32 |
139 |
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PO4H3251 RLPH3201 |
32 |
131 |
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PO4E4251 RLPE4201 |
32 |
131 |
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PO4J5251 RLPJ5201 |
32 |
131 |
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PO4B3251 RLPB3201 |
32 |
134 |
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PO4C5251 RLPC5201 |
32 |
134 |
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PO4G1251 RLPG1201 |
32 |
137 |
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PO4A4251 RLPA4201 |
32 |
135 |
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PO4A2251 RLPA2201 |
32 |
136 |
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PO483251 RLP83201 |
32 |
130 |
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PO4F1251 RLPF1201 |
32 |
136 |
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PO4C1251 RLPC1201 |
32 |
132 |
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PO4J4251 RLPJ4201 |
32 |
127 |
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PO4J2251 RLPJ2201 |
32 |
131 |
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PO4I1251 RLPI1201 |
32 |
133 |
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PO4D2251 RLPD2201 |
32 |
133 |
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PO4E1251 RLPE1201 |
32 |
133 |
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PO4I3251 RLPI3201 |
32 |
135 |
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PO4G5251 RLPG5201 |
32 |
136 |
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PO494251 RLP94201 |
32 |
129 |
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PO4H1251 RLPH1201 |
32 |
137 |
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PO481251 RLP81201 |
32 |
132 |
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PO4I4251 RLPI4201 |
32 |
132 |
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PO4B1251 RLPB1201 |
32 |
133 |
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PO492251 RLP92201 |
32 |
129 |
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PO4E5251 RLPE5201 |
32 |
130 |
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PO4G2251 RLPG2201 |
32 |
137 |
1nqu |
PO4J2251 RDLJ2201 |
28 |
124 |
Details |
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PO4G3251 RDLG3201 |
28 |
121 |
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PO485251 RDL85201 |
28 |
126 |
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PO4G1251 RDLG1201 |
28 |
126 |
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PO4D1251 RDLD1201 |
28 |
124 |
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PO4F3251 RDLF3201 |
28 |
121 |
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PO4B4251 RDLB4201 |
28 |
126 |
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PO4J4251 RDLJ4201 |
28 |
128 |
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PO4D5251 RDLD5201 |
28 |
125 |
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PO492251 RDL92201 |
28 |
126 |
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PO4I3251 RDLI3201 |
28 |
125 |
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PO4G5251 RDLG5201 |
28 |
123 |
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PO4I2251 RDLI2201 |
28 |
128 |
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PO4G4251 RDLG4201 |
28 |
128 |
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PO495251 RDL95201 |
28 |
124 |
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PO4I5251 RDLI5201 |
28 |
125 |
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PO4D3251 RDLD3201 |
28 |
125 |
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PO4H3251 RDLH3201 |
28 |
121 |
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PO4B2251 RDLB2201 |
28 |
126 |
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PO4J3251 RDLJ3201 |
28 |
121 |
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PO481251 RDL81201 |
28 |
124 |
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PO4D4251 RDLD4201 |
28 |
122 |
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PO4C3251 RDLC3201 |
28 |
123 |
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PO4H5251 RDLH5201 |
28 |
124 |
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PO4B3251 RDLB3201 |
28 |
124 |
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PO4H2251 RDLH2201 |
28 |
125 |
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PO4C1251 RDLC1201 |
28 |
124 |
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PO493251 RDL93201 |
28 |
124 |
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PO4F4251 RDLF4201 |
28 |
128 |
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PO4E1251 RDLE1201 |
28 |
127 |
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PO4C4251 RDLC4201 |
28 |
123 |
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PO4F5251 RDLF5201 |
28 |
124 |
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PO4C2251 RDLC2201 |
28 |
117 |
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PO4A2251 RDLA2201 |
28 |
127 |
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PO4I4251 RDLI4201 |
28 |
122 |
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PO4G2251 RDLG2201 |
28 |
124 |
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PO4H4251 RDLH4201 |
28 |
128 |
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PO4E4251 RDLE4201 |
28 |
122 |
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PO4E3251 RDLE3201 |
28 |
128 |
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PO482251 RDL82201 |
28 |
117 |
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PO484251 RDL84201 |
28 |
123 |
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PO491251 RDL91201 |
28 |
125 |
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PO4E5251 RDLE5201 |
28 |
120 |
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PO4A3251 RDLA3201 |
28 |
123 |
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PO4I1251 RDLI1201 |
28 |
124 |
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PO4A4251 RDLA4201 |
28 |
128 |
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PO4A6251 RDLA6201 |
28 |
120 |
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PO4C5251 RDLC5201 |
28 |
126 |
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PO4D2251 RDLD2201 |
28 |
128 |
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PO494251 RDL94201 |
28 |
126 |
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PO4J1251 RDLJ1201 |
28 |
126 |
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PO4A5251 RDLA5201 |
28 |
122 |
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PO4H1251 RDLH1201 |
28 |
127 |
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PO4F1251 RDLF1201 |
28 |
127 |
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PO4F2251 RDLF2201 |
28 |
125 |
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PO483251 RDL83201 |
28 |
123 |
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PO4E2251 RDLE2201 |
28 |
123 |
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PO4B1251 RDLB1201 |
28 |
125 |
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PO4J5251 RDLJ5201 |
28 |
123 |
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PO4B5251 RDLB5201 |
28 |
124 |
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v7.0 March 2009 |
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: 0.6628 seconds |