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 F1300
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 C1300
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
NAJ I1300
23G GLY
25G ALA
26G GLY
27G GLY
28G ILE
29G GLY
46G ALA
47G ASP
48G ILE
49G ALA
71G CYS
72G ASP
73G VAL
74G THR
99G ASN
100G VAL
101G GLY
102G VAL
103G LEU
124G ILE
151G THR
152G ALA
153G SER
167G TYR
171G LYS
197G PRO
198G TYR
199G ILE
200G VAL
202G SER
203G PRO
NAJ L1300
23J GLY
25J ALA
26J GLY
27J GLY
28J ILE
29J GLY
46J ALA
47J ASP
48J ILE
49J ALA
71J CYS
72J ASP
73J VAL
74J THR
99J ASN
100J VAL
101J GLY
102J VAL
103J LEU
124J ILE
151J THR
152J ALA
153J SER
167J TYR
171J LYS
197J PRO
198J TYR
199J ILE
200J VAL
202J SER
203J PRO
MAX E6001
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
266J ASN
269J PHE
270J PRO
273J LEU
MAX B6001
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
266G ASN
269G PHE
270G PRO
273G LEU
MAX H6001
103G LEU
104G SER
106G THR
153G SER
154G ILE
155G SER
162G GLY
163G VAL
164G SER
167G TYR
197G PRO
198G TYR
199G ILE
216G VAL
262G TYR
266A ASN
269A PHE
270A PRO
273A LEU
MAX K6001
103J LEU
104J SER
106J THR
153J SER
154J ILE
155J SER
162J GLY
163J VAL
164J SER
167J TYR
197J PRO
198J TYR
199J ILE
216J VAL
262J TYR
266D ASN
269D PHE
270D PRO
273D 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):

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 NAJF1300 Details
NAJB1300
NAJH1300
NAJD1300
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
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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