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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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| 1nxd |
| METAL BINDING PROTEIN |
HEADER |
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| CRYSTAL STRUCTURE OF MNMN CONCANAVALIN A |
TITLE |
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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) |
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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) |
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| AZI Q 910 |
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| 54 | A |
TYR |
| 113 | A |
SER |
| 114 | A |
LYS |
| 115 | A |
LEU |
| 180 | A |
HIS |
| 181 | A |
ILE |
| 189 | A |
ALA |
| 190 | A |
SER |
| 191 | A |
PHE |
| AZI V 910 |
|---|
| 54 | F |
TYR |
| 113 | F |
SER |
| 114 | F |
LYS |
| 115 | F |
LEU |
| 180 | F |
HIS |
| 181 | F |
ILE |
| 189 | F |
ALA |
| 190 | F |
SER |
| 191 | F |
PHE |
| AZI R 913 |
|---|
| 88 | A |
TRP |
| 115 | A |
LEU |
| 124 | A |
ASN |
| 130 | U |
PHE |
| | 134 | U |
SER |
| 137 | U |
GLN |
| 139 | U |
ASP |
| 180 | A |
HIS |
| 183 | A |
GLU |
| AZI W 913 |
|---|
| 88 | F |
TRP |
| 115 | F |
LEU |
| 124 | F |
ASN |
| 130 | Z |
PHE |
| 134 | Z |
SER |
| 137 | Z |
GLN |
| 139 | Z |
ASP |
| 180 | F |
HIS |
| 183 | F |
GLU |
| GOL G 812 |
|---|
| 113 | A |
SER |
| 115 | A |
LEU |
| 124 | A |
ASN |
| 125 | A |
ALA |
| 126 | A |
LEU |
| 128 | U |
PHE |
| 129 | U |
MET |
| 130 | U |
PHE |
| 139 | U |
ASP |
| | 178 | A |
PRO |
| 179 | A |
VAL |
| 180 | A |
HIS |
| GOL L 812 |
|---|
| 113 | F |
SER |
| 115 | F |
LEU |
| 124 | F |
ASN |
| 125 | F |
ALA |
| 126 | F |
LEU |
| 128 | Z |
PHE |
| 129 | Z |
MET |
| 130 | Z |
PHE |
| 139 | Z |
ASP |
| 178 | F |
PRO |
| 179 | F |
VAL |
| 180 | F |
HIS |
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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: LigPlot (hosted at the EBI):
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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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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) |
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| pdb ID |
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| 1dq0 |
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Details |
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| pdb ID |
Ligand Unique ID |
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| 1tei |
MANA_243 NAGC_240 MANB_242 MANZ_241 NAGD_244 |
Details |
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MANT_241 MANU_243 NAGW_240 MANV_242 |
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MANL_241 NAGO_240 NAGP_244 MANN_242 MANM_243 |
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MANH_241 NAGK_240 MANI_243 MANJ_242 |
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MANB_241 MANC_243 NAGE_240 MAND_242 |
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MAND_241 MANE_243 MANF_242 NAGG_240 |
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MANR_241 MANS_243 NAGU_240 MANT_242 |
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MANJ_241 NAGM_240 MANL_242 NAGN_244 MANK_243 |
| 1jn2 |
SFPD1001 |
Details |
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SFPP1001 |
| 1ona |
MANP_240 MMAR_241 MANQ_242 |
Details |
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MANJ_240 MANK_242 MMAL_241 |
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MAND_240 MMAF_241 MANE_242 |
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MANV_240 MMAX_241 MANW_242 |
| 1bxh |
AMGQ_242 AMGR_241 |
Details |
| 1cjp |
MUGL_240 |
Details |
| 3d4k |
H1MA_241 MANF_242 MANE_240 |
Details |
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H1MG_241 MANK_240 MANL_242 |
| 1cvn |
MANP_240 MANQ_242 MANR_241 |
Details |
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MANJ_240 MANL_241 MANK_242 |
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MANV_240 MANX_241 MANW_242 |
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MAND_240 MANF_241 MANE_242 |
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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) |
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| AZI |
NAME: |
AZIDE ION |
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FORMULA: |
N3 |
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SMILES: |
[N-]=[N+]=[N-] |
| GOL |
NAME: |
GLYCEROL |
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FORMULA: |
C3 H8 O3 |
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SMILES: |
OCC(O)CO |
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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 |
| Script execution time: 0.9726 seconds |