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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1pjc
OXIDOREDUCTASE HEADER
L-ALANINE DEHYDROGENASE COMPLEXED WITH NAD TITLE
PROTEIN (L-ALANINE 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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NAD G 500
129A LEU
132A MET
133A SER
136A ALA
173A LEU
174A GLY
175A GLY
176A GLY
177A VAL
178A VAL
196A PHE
197A ASP
198A ILE
199A ASN
202A ARG
219A SER
237A ALA
238A VAL
239A LEU
240A VAL
246A PRO
248A LEU
266A VAL
267A ALA
268A VAL
269A ASP
270A GLN
298A PRO
299A ASN
300A MET
301A PRO
NAD K 500
129E LEU
132E MET
133E SER
136E ALA
173E LEU
174E GLY
175E GLY
176E GLY
177E VAL
178E VAL
196E PHE
197E ASP
198E ILE
199E ASN
202E ARG
219E SER
237E ALA
238E VAL
239E LEU
240E VAL
246E PRO
248E LEU
266E VAL
267E ALA
268E VAL
269E ASP
270E GLN
298E PRO
299E ASN
300E MET
301E PRO
NAD I 500
132C MET
133C SER
136C ALA
173C LEU
174C GLY
175C GLY
176C GLY
177C VAL
178C VAL
196C PHE
197C ASP
198C ILE
199C ASN
202C ARG
219C SER
237C ALA
238C VAL
239C LEU
240C VAL
246C PRO
248C LEU
266C VAL
267C ALA
268C VAL
269C ASP
270C GLN
298C PRO
299C ASN
300C MET
301C PRO
NAD H 500
132B MET
133B SER
136B ALA
173B LEU
174B GLY
175B GLY
176B GLY
177B VAL
178B VAL
196B PHE
197B ASP
198B ILE
199B ASN
202B ARG
219B SER
237B ALA
238B VAL
239B LEU
240B VAL
246B PRO
248B LEU
266B VAL
267B ALA
268B VAL
269B ASP
270B GLN
298B PRO
299B ASN
300B MET
301B PRO
NAD J 500
132D MET
133D SER
136D ALA
173D LEU
174D GLY
175D GLY
176D GLY
177D VAL
178D VAL
196D PHE
197D ASP
198D ILE
199D ASN
202D ARG
219D SER
237D ALA
238D VAL
239D LEU
240D VAL
246D PRO
248D LEU
266D VAL
267D ALA
268D VAL
269D ASP
270D GLN
298D PRO
299D ASN
300D MET
301D PRO
NAD L 500
132F MET
133F SER
136F ALA
173F LEU
174F GLY
175F GLY
176F GLY
177F VAL
178F VAL
196F PHE
197F ASP
198F ILE
199F ASN
202F ARG
219F SER
237F ALA
238F VAL
239F LEU
240F VAL
246F PRO
248F LEU
266F VAL
267F ALA
268F VAL
269F ASP
270F GLN
298F PRO
299F ASN
300F MET
301F PRO
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):

» Jmol
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
1pjb 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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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
v3.0
January 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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