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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2b3d
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF MODULATOR OF DRUG ACTIVITY B IN COMPLEX WITH FLAVIN ADENINE DINUCLEOTIDE TITLE
MODULATOR OF DRUG ACTIVITY B 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 D1206
21C ALA
22C LYS
24C PHE
25C ALA
26C HIS
27C SER
28C ASN
29C GLY
30C GLN
31C LEU
32C ASN
34C THR
79C PRO
80C GLY
81C TRP
82C TRP
83C MET
94A ASP
98A THR
119A TYR
135C THR
136C TRP
137C ASN
138C ALA
168A PHE
182C VAL
183C ILE
186C PRO
188C VAL
191C TYR
FAD B1205
22A LYS
24A PHE
25A ALA
26A HIS
27A SER
28A ASN
29A GLY
30A GLN
31A LEU
32A ASN
34A THR
79A PRO
80A GLY
81A TRP
82A TRP
83A MET
94C ASP
98C THR
119C TYR
135A THR
136A TRP
137A ASN
138A ALA
168C PHE
182A VAL
183A ILE
186A PRO
188A VAL
191A TYR
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
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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.

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apo-structure
pdb ID
2amj Details
other holo-structures
pdb ID Ligand Unique ID
none
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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