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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2bgm
XIDOREDUCTASE HEADER
X-RAY STRUCTURE OF TERNARY-SECOISOLARICIRESINOL DEHYDROGENASE TITLE
RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE 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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NAJ B1300
23B GLY
25B ALA
26B GLY
27B GLY
28B ILE
29B GLY
46B ALA
47B ASP
48B ILE
49B ALA
71B CYS
72B ASP
73B VAL
74B THR
99B ASN
100B VAL
101B GLY
102B VAL
103B LEU
124B ILE
151B THR
152B ALA
153B SER
167B TYR
171B LYS
197B PRO
198B TYR
199B ILE
200B VAL
202B SER
203B PRO
NAJ C1300
23C GLY
25C ALA
26C GLY
27C GLY
28C ILE
29C GLY
46C ALA
47C ASP
48C ILE
49C ALA
71C CYS
72C ASP
73C VAL
74C THR
99C ASN
100C VAL
101C GLY
102C VAL
103C LEU
124C ILE
151C THR
152C ALA
153C SER
167C TYR
171C LYS
197C PRO
198C TYR
199C ILE
200C VAL
202C SER
203C PRO
NAJ D1300
23D GLY
25D ALA
26D GLY
27D GLY
28D ILE
29D GLY
46D ALA
47D ASP
48D ILE
49D ALA
71D CYS
72D ASP
73D VAL
74D THR
99D ASN
100D VAL
101D GLY
102D VAL
103D LEU
124D ILE
151D THR
152D ALA
153D SER
167D TYR
171D LYS
197D PRO
198D TYR
199D ILE
200D VAL
202D SER
203D PRO
NAJ A1300
23A GLY
25A ALA
26A GLY
27A GLY
28A ILE
29A GLY
46A ALA
47A ASP
48A ILE
49A ALA
71A CYS
72A ASP
73A VAL
74A THR
99A ASN
100A VAL
101A GLY
102A VAL
103A LEU
124A ILE
151A THR
152A ALA
153A SER
167A TYR
171A LYS
197A PRO
198A TYR
199A ILE
200A VAL
202A SER
203A PRO
MAX C6001
103C LEU
104C SER
106C THR
153C SER
154C ILE
155C SER
162C GLY
163C VAL
164C SER
167C TYR
197C PRO
198C TYR
199C ILE
216C VAL
262C TYR
266D ASN
269D PHE
270D PRO
273D LEU
MAX B6001
103B LEU
104B SER
106B THR
153B SER
154B ILE
155B SER
162B GLY
163B VAL
164B SER
167B TYR
197B PRO
198B TYR
199B ILE
216B VAL
262B TYR
266A ASN
269A PHE
270A PRO
273A LEU
MAX A6001
103A LEU
104A SER
106A THR
153A SER
154A ILE
155A SER
162A GLY
163A VAL
164A SER
167A TYR
197A PRO
198A TYR
199A ILE
216A VAL
262A TYR
266B ASN
269B PHE
270B PRO
273B LEU
MAX D6001
103D LEU
104D SER
106D THR
153D SER
154D ILE
155D SER
162D GLY
163D VAL
164D SER
167D TYR
197D PRO
198D TYR
199D ILE
216D VAL
262D TYR
266C ASN
269C PHE
270C PRO
273C LEU
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):

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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
2bgk Details
other holo-structures
pdb ID Ligand Unique ID
2bgl NAJB1300 Details
NAJC1300
NAJD1300
NAJA1300
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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MAX NAME: Matairesinol
FORMULA: C20 H23 O6
SMILES: COc1cc(CC2COC(=O)C2Cc3ccc(O)c(OC)c3)ccc1O
NAJ NAME: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
FORMULA: C21 H27 N7 O14 P2
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP([O-])(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)[nH+]cnc45)C(O)C2O
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
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