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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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2b15 |
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THE CRYSTAL STRUCTURE OF 2,4-DINITROPHENOL IN COMPLEX WITH HUMAN TRANSTHYRETIN |
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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DNF C 130 |
15 | G |
LYS |
17 | G |
LEU |
108 | G |
ALA |
109 | G |
ALA |
110 | A |
LEU |
117 | A |
SER |
118 | A |
THR |
119 | G |
THR |
DNF I 130 |
15 | A |
LYS |
17 | A |
LEU |
108 | A |
ALA |
109 | A |
ALA |
110 | G |
LEU |
| 117 | G |
SER |
118 | G |
THR |
119 | A |
THR |
DNF F 128 |
15 | J |
LYS |
17 | D |
LEU |
108 | J |
ALA |
109 | D |
ALA |
110 | D |
LEU |
117 | D |
SER |
118 | D |
THR |
119 | J |
THR |
DNF L 128 |
15 | D |
LYS |
17 | J |
LEU |
| 108 | D |
ALA |
109 | J |
ALA |
110 | J |
LEU |
117 | J |
SER |
118 | J |
THR |
119 | D |
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: 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 |
3cbr |
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Details |
pdb ID |
Ligand Unique ID |
2f7i |
26CD_325 26CH_325 |
Details |
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26CB_326 26CF_326 |
1z7j |
T4AD_129 T4AH_129 |
Details |
1y1d |
FHIB2000 FHIF2000 |
Details |
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FHID3000 FHIH3000 |
3cn3 |
LJ4A_128 LJ4C_128 |
Details |
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LJ4B_128 LJ4D_128 |
1tz8 |
DESJ_128 |
Details |
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DESL_128 |
1e5a |
TBPB_999 TBPF_999 |
Details |
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TBPD_998 TBPH_998 |
3ipb |
JZDA_128 |
Details |
2qgd |
MR5D_201 MR5H_201 |
Details |
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MR5B_200 MR5F_200 |
2b77 |
3CAD_239 3CAH_239 |
Details |
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3CAB_240 3CAF_240 |
1tt6 |
DESB_128 DESG_128 |
Details |
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DESK_129 DESL_129 |
3ipe |
JZEB_128 |
Details |
1e4h |
PBRF_998 PBRL_998 |
Details |
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PBRC_999 PBRI_999 |
1tyr |
READ_130 REAH_130 |
Details |
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REAB_131 REAF_131 |
3b56 |
DIUB2000 DIUF2000 |
Details |
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DIUD3000 DIUH3000 |
1u21 |
P2CC_211 P2CD_211 |
Details |
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P2CG_221 P2CH_221 |
2fbr |
44CB_173 44CE_173 |
Details |
3d2t |
1FLB_502 1FLF_502 |
Details |
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1FLD_500 1FLH_500 |
2roy |
P28B_128 P28F_128 |
Details |
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P28D_128 P28H_128 |
3hj0 |
A93B_128 A93D_128 |
Details |
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A93A_128 A93C_128 |
2gab |
NE2G_502 NE2H_502 |
Details |
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NE2C_501 NE2D_501 |
2f8i |
205D1001 205H1001 |
Details |
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205B1002 205F1002 |
3gs4 |
7BDB_500 7BDD_500 |
Details |
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7BDA_501 7BDC_501 |
2qge |
MR6D_200 MR6H_200 |
Details |
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MR6B_201 MR6F_201 |
3kgu |
GEND3071 GENH3071 |
Details |
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GENB3071 GENF3071 |
2flm |
6CAB_201 6CAE_201 |
Details |
2g9k |
NE1D_500 NE1H_500 |
Details |
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NE1B_501 NE1F_501 |
2qgc |
MR4D_128 MR4H_128 |
Details |
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MR4B_128 MR4F_128 |
2g5u |
PCQC_240 PCQD_240 |
Details |
2rox |
T44E_128 T44J_128 |
Details |
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T44C_128 T44H_128 |
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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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DNF |
NAME: |
2,4-DINITROPHENOL |
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FORMULA: |
C6 H4 N2 O5 |
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SMILES: |
Oc1ccc(cc1[N+]([O-])=O)[N+]([O-])=O |
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v9.4 March 2011 |
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: 4.2101 seconds |