university lille north of france LigASite database of binding sites

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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Illustration of Binding SiteHelp

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.

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HETgroup - Residue ContactsHelp

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.

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SAH A 481
150A TYR
151A PHE
154A TYR
160A GLN
163A MET
164A MET
169A ARG
191A ASP
192A VAL
193A GLY
194A CYS
195A GLY
196A SER
198A ILE
199A LEU
214A VAL
215A GLU
216A ALA
217A SER
241A GLY
242A LYS
243A VAL
244A GLU
258A GLU
269A MET
272A SER
SAH C 481
150C TYR
151C PHE
154C TYR
160C GLN
163C MET
164C MET
169C ARG
191C ASP
192C VAL
193C GLY
194C CYS
195C GLY
196C SER
198C ILE
199C LEU
214C VAL
215C GLU
216C ALA
217C SER
241C GLY
242C LYS
243C VAL
244C GLU
258C GLU
267C GLU
269C MET
272C SER
SAH D 481
150D TYR
151D PHE
154D TYR
160D GLN
163D MET
164D MET
169D ARG
191D ASP
192D VAL
193D GLY
194D CYS
195D GLY
196D SER
198D ILE
199D LEU
214D VAL
215D GLU
216D ALA
217D SER
241D GLY
242D LYS
243D VAL
244D GLU
258D GLU
267D GLU
269D MET
272D SER
SAH E 481
150E TYR
151E PHE
154E TYR
160E GLN
163E MET
164E MET
169E ARG
191E ASP
192E VAL
193E GLY
194E CYS
195E GLY
196E SER
198E ILE
199E LEU
214E VAL
215E GLU
216E ALA
217E SER
241E GLY
242E LYS
243E VAL
244E GLU
258E GLU
269E MET
272E SER
SAH F 481
150F TYR
151F PHE
154F TYR
160F GLN
163F MET
164F MET
169F ARG
191F ASP
192F VAL
193F GLY
194F CYS
195F GLY
196F SER
198F ILE
199F LEU
214F VAL
215F GLU
216F ALA
217F SER
241F GLY
242F LYS
243F VAL
244F GLU
258F GLU
267F GLU
269F MET
272F SER
SAH G 481
150G TYR
151G PHE
154G TYR
160G GLN
163G MET
164G MET
169G ARG
191G ASP
192G VAL
193G GLY
194G CYS
195G GLY
196G SER
198G ILE
199G LEU
214G VAL
215G GLU
216G ALA
217G SER
241G GLY
242G LYS
243G VAL
244G GLU
258G GLU
269G MET
272G SER
SAH B 481
150B TYR
151B PHE
154B TYR
160B GLN
163B MET
164B MET
169B ARG
191B ASP
192B VAL
193B GLY
194B CYS
195B GLY
196B SER
198B ILE
199B LEU
214B VAL
215B GLU
216B ALA
217B SER
241B GLY
242B LYS
243B VAL
244B GLU
258B GLU
267B GLU
269B MET
272B SER
SAH H 481
150H TYR
151H PHE
154H TYR
160H GLN
163H MET
164H MET
169H ARG
191H ASP
192H VAL
193H GLY
194H CYS
195H GLY
196H SER
198H ILE
199H LEU
214H VAL
215H GLU
216H ALA
217H SER
241H GLY
242H LYS
243H VAL
244H GLU
258H GLU
267H GLU
269H MET
272H SER
External LinksHelp

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.

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Links to external databases:

LigPlot (hosted at the EBI):

Download FilesHelp

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.

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Hide table of related structures

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).

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pdb ID
3b3g Details
other holo-structures
pdb ID Ligand Unique ID
Ligand ListHelp

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

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FORMULA: C14 H20 N6 O5 S1
SMILES: NC(CCSCC1OC(C(O)C1O)[n]2cnc3c(N)ncnc23)C(O)=O
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
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