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

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

(click anywhere in this window to remove it)
2q2v
OXIDOREDUCTASE HEADER
STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA TITLE
BETA-D-HYDROXYBUTYRATE 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
NAD E 300
12D GLY
14D THR
15D SER
16D GLY
17D ILE
35D ASN
36D GLY
37D PHE
59D ALA
60D ASP
61D LEU
62D SER
87D ASN
88D ALA
89D GLY
90D ILE
106D LYS
110D LEU
137D ILE
138D ALA
139D SER
140D VAL
141D HIS
152D TYR
156D LYS
182D PRO
183D GLY
184D TRP
185D VAL
187D THR
188D PRO
189D LEU
190D VAL
NAD C 300
12B GLY
14B THR
15B SER
16B GLY
17B ILE
35B ASN
36B GLY
37B PHE
59B ALA
60B ASP
61B LEU
62B SER
87B ASN
88B ALA
89B GLY
90B ILE
106B LYS
110B LEU
111B ASN
137B ILE
138B ALA
139B SER
140B VAL
141B HIS
152B TYR
156B LYS
182B PRO
183B GLY
184B TRP
185B VAL
187B THR
188B PRO
189B LEU
190B VAL
NAD G 300
12F GLY
14F THR
15F SER
16F GLY
17F ILE
35F ASN
36F GLY
37F PHE
59F ALA
60F ASP
61F LEU
62F SER
87F ASN
88F ALA
89F GLY
90F ILE
102A GLU
110F LEU
111F ASN
137F ILE
138F ALA
139F SER
140F VAL
152F TYR
156F LYS
182F PRO
183F GLY
184F TRP
185F VAL
187F THR
188F PRO
189F LEU
190F 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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
2q2w Details
other holo-structures
pdb ID Ligand Unique ID
2q2q NADH_300 Details
NADF_300
NADB_300
NADD_300
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.

(click anywhere in this window to remove it)
NAD NAME: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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)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
Script execution time: 0.1187 seconds