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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1b15
OXIDOREDUCTASE HEADER
ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-ACETONE TITLE
ALCOHOL 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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NAE D 256
11C VAL
12C ALA
14C LEU
15C GLY
16C GLY
17C ILE
18C GLY
37C ASP
38C ARG
39C VAL
62C TYR
63C ASP
64C VAL
91C GLY
92C ALA
93C GLY
94C ILE
95C LEU
102C ARG
106C ILE
136C ILE
137C CYS
138C SER
139C VAL
140C THR
145C ILE
151C TYR
155C LYS
181C PRO
182C GLY
183C ILE
184C THR
186C THR
187C PRO
188C LEU
189C VAL
206C LEU
NAE B 255
11A VAL
12A ALA
14A LEU
15A GLY
16A GLY
17A ILE
18A GLY
37A ASP
38A ARG
39A VAL
62A TYR
63A ASP
64A VAL
91A GLY
92A ALA
93A GLY
94A ILE
95A LEU
102A ARG
106A ILE
136A ILE
137A CYS
138A SER
139A VAL
140A THR
145A ILE
151A TYR
155A LYS
181A PRO
182A GLY
183A ILE
184A THR
186A THR
187A PRO
188A LEU
189A VAL
206A 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
1a4u Details
other holo-structures
pdb ID Ligand Unique ID
1b16 NAQD_500 Details
NAQB_600
1b2l CYHA_256 NDCB_255 DTTC_257 Details
CYHD_256 NDCE_255 DTTF_257
1sby ETFF2256 NADE2255 Details
ETFC1256 NADB1255
1b14 NADB_255 Details
NADD_256
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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NAE NAME: NICOTINAMIDE ADENINE DINUCLEOTIDE ACETONE ADDUCT
FORMULA: C24 H31 N7 O15 P2
SMILES: CC(=O)Cc1cc[n+](cc1C(N)=O)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)ncnc45)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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