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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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| 2au8 |
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| CATALYTIC INTERMEDIATE STRUCTURE OF INORGANIC PYROPHOSPHATASE |
TITLE |
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| INORGANIC PYROPHOSPHATASE |
COMPND |
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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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| MN J 202 |
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| 20 | D |
GLU |
| 29 | D |
LYS |
| 31 | D |
GLU |
| 55 | D |
TYR |
| 56 | D |
GLY |
| 57 | D |
TYR |
| 67 | D |
ASP |
| 68 | D |
PRO |
| 70 | D |
ASP |
| MN I 202 |
|---|
| 20 | C |
GLU |
| 29 | C |
LYS |
| 31 | C |
GLU |
| 55 | C |
TYR |
| 56 | C |
GLY |
| 57 | C |
TYR |
| 67 | C |
ASP |
| 68 | C |
PRO |
| 70 | C |
ASP |
| PO4 J 180 |
|---|
| 29 | D |
LYS |
| 31 | D |
GLU |
| 43 | D |
ARG |
| 55 | D |
TYR |
| | 65 | D |
ASP |
| 67 | D |
ASP |
| 70 | D |
ASP |
| 102 | D |
ASP |
| 104 | D |
LYS |
| MN J 204 |
|---|
| 29 | D |
LYS |
| 31 | D |
GLU |
| 42 | D |
ASP |
| 43 | D |
ARG |
| 65 | D |
ASP |
| 67 | D |
ASP |
| PO4 I 180 |
|---|
| 29 | C |
LYS |
| 31 | C |
GLU |
| 43 | C |
ARG |
| 55 | C |
TYR |
| 65 | C |
ASP |
| 67 | C |
ASP |
| 70 | C |
ASP |
| 102 | C |
ASP |
| 104 | C |
LYS |
| MN I 204 |
|---|
| 29 | C |
LYS |
| 31 | C |
GLU |
| | 42 | C |
ASP |
| 43 | C |
ARG |
| 65 | C |
ASP |
| 67 | C |
ASP |
| MN J 203 |
|---|
| 43 | D |
ARG |
| 65 | D |
ASP |
| 97 | D |
ASP |
| 99 | D |
ALA |
| 102 | D |
ASP |
| 141 | D |
TYR |
| 142 | D |
LYS |
| MN I 203 |
|---|
| 43 | C |
ARG |
| 65 | C |
ASP |
| 97 | C |
ASP |
| 99 | C |
ALA |
| 102 | C |
ASP |
| 141 | C |
TYR |
| 142 | C |
LYS |
| CL J 208 |
|---|
| 55 | D |
TYR |
| 95 | D |
MET |
| 97 | D |
ASP |
| 102 | D |
ASP |
| | 104 | D |
LYS |
| 138 | D |
PHE |
| 141 | D |
TYR |
| 142 | D |
LYS |
| CL I 208 |
|---|
| 55 | C |
TYR |
| 95 | C |
MET |
| 97 | C |
ASP |
| 102 | C |
ASP |
| 104 | C |
LYS |
| 138 | C |
PHE |
| 141 | C |
TYR |
| 142 | C |
LYS |
| MN J 201 |
|---|
| 63 | D |
SER |
| 65 | D |
ASP |
| 68 | D |
PRO |
| 70 | D |
ASP |
| 102 | D |
ASP |
| MN I 201 |
|---|
| 63 | C |
SER |
| 65 | C |
ASP |
| 68 | C |
PRO |
| 70 | C |
ASP |
| 102 | C |
ASP |
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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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| 1igp |
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Details |
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| pdb ID |
Ligand Unique ID |
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| 2au6 |
POPJ_182 _MNJ_204 __FJ_211 _MNJ_203 _MNJ_202 _MNJ_201 |
Details |
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POPL_182 _MNL_201 _MNL_202 _MNL_204 _MNL_203 __FL_211 |
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POPI_182 _MNI_201 _MNI_204 _MNI_203 _MNI_202 __FI_211 |
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POPK_182 _MNK_201 _MNK_204 _MNK_202 _MNK_203 __FK_211 |
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POPG_182 _MNG_202 _MNG_203 _MNG_201 _MNG_204 __FG_211 |
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POPH_182 _MNH_203 __FH_211 _MNH_204 _MNH_202 _MNH_201 |
| 2auu |
POPK_180 _MGK_202 _MGK_204 _MGK_203 _MGK_201 __FK_211 |
Details |
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POPL_180 _MGL_202 _MGL_201 _MGL_203 __FL_211 _MGL_204 |
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POPI_180 _MGI_202 _MGI_201 _MGI_203 _MGI_204 __FI_211 |
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POPJ_180 _MGJ_201 __FJ_211 _MGJ_202 _MGJ_203 _MGJ_204 |
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POPH_180 _MGH_202 _MGH_201 __FH_211 _MGH_204 _MGH_203 |
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POPG_180 _MGG_203 _MGG_202 __FG_211 _MGG_204 _MGG_201 |
| 2au9 |
POPH_180 _MNH_203 __FH_211 _CLH_208 _MNH_204 _MNH_202 _MNH_201 |
Details |
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POPL_180 _MNL_201 _MNL_202 _MNL_204 _CLL_208 _MNL_203 __FL_211 |
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POPK_180 _MNK_201 _MNK_204 _MNK_202 _MNK_203 _CLK_208 __FK_211 |
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POPJ_180 _CLJ_208 _MNJ_204 __FJ_211 _MNJ_203 _MNJ_202 _MNJ_201 |
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POPG_180 _MNG_202 _CLG_208 _MNG_203 _MNG_201 _MNG_204 __FG_211 |
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POPI_180 _MNI_201 _MNI_204 _MNI_203 _MNI_202 _CLI_208 __FI_211 |
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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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| PO4 |
NAME: |
PHOSPHATE ION |
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FORMULA: |
O4 P1 |
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SMILES: |
[O-]P([O-])([O-])=O |
| CL |
NAME: |
CHLORIDE ION |
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FORMULA: |
CL1 |
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SMILES: |
[Cl-] |
| MN |
NAME: |
MANGANESE (II) ION |
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FORMULA: |
MN1 |
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SMILES: |
[Mn++] |
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v6.0
October 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 |
| Script execution time: 0.8007 seconds |