university lille north of france LigASite database of binding sites
holo-structureHelp

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

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2oal
BIOSYNTHETIC PROTEIN, FLAVOPROTEIN HEADER
REBH WITH BOUND FAD TITLE
TRYPTOPHAN HALOGENASE COMPND
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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FAD E 601
11D VAL
12D GLY
13D GLY
14D GLY
15D THR
16D ALA
17D GLY
37D LEU
38D GLN
39D ALA
41D ASP
47D VAL
48D GLY
49D GLU
50D ALA
51D THR
173D ALA
195D ASP
196D ARG
197D VAL
227D CYS
228D SER
229D GLY
230D PHE
231D ARG
233D LEU
255D ALA
284D TRP
286D ILE
328D ILE
330D PHE
346D ILE
347D GLY
348D THR
352D PHE
355D PRO
358D SER
359D THR
360D GLY
361D ILE
362D TYR
364D VAL
FAD B 600
11A VAL
12A GLY
13A GLY
14A GLY
15A THR
16A ALA
17A GLY
37A LEU
38A GLN
39A ALA
41A ASP
47A VAL
48A GLY
49A GLU
50A ALA
51A THR
173A ALA
195A ASP
196A ARG
197A VAL
227A CYS
228A SER
229A GLY
230A PHE
231A ARG
233A LEU
255A ALA
284A TRP
286A ILE
328A ILE
330A PHE
346A ILE
347A GLY
348A THR
352A PHE
355A PRO
358A SER
360A GLY
361A ILE
362A TYR
364A VAL
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
Help

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.

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apo-structure
pdb ID
2oam Details
other holo-structures
pdb ID Ligand Unique ID
2e4g TRPA1001 Details
TRPB1000
2oa1 ADNE2005 Details
FADB2004 _CLC2001
TRPA2002
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 www.rcsb.org.

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FAD NAME: FLAVIN-ADENINE DINUCLEOTIDE
FORMULA: C27 H33 N9 O15 P2
SMILES: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CC(O)C(O)C(O)COP(O)(=O)OP(O)(=O)OCC4OC(C(O)C4O)[n]5cnc6c(N)ncnc56)c2cc1C
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
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