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 B 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 H 500
129G LEU
132G MET
133G SER
136G ALA
173G LEU
174G GLY
175G GLY
176G GLY
177G VAL
178G VAL
196G PHE
197G ASP
198G ILE
199G ASN
202G ARG
219G SER
237G ALA
238G VAL
239G LEU
240G VAL
246G PRO
248G LEU
266G VAL
267G ALA
268G VAL
269G ASP
270G GLN
298G PRO
299G ASN
300G MET
301G PRO
NAD F 500
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 D 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 J 500
132I MET
133I SER
136I ALA
173I LEU
174I GLY
175I GLY
176I GLY
177I VAL
178I VAL
196I PHE
197I ASP
198I ILE
199I ASN
202I ARG
219I SER
237I ALA
238I VAL
239I LEU
240I VAL
246I PRO
248I LEU
266I VAL
267I ALA
268I VAL
269I ASP
270I GLN
298I PRO
299I ASN
300I MET
301I PRO
NAD L 500
132K MET
133K SER
136K ALA
173K LEU
174K GLY
175K GLY
176K GLY
177K VAL
178K VAL
196K PHE
197K ASP
198K ILE
199K ASN
202K ARG
219K SER
237K ALA
238K VAL
239K LEU
240K VAL
246K PRO
248K LEU
266K VAL
267K ALA
268K VAL
269K ASP
270K GLN
298K PRO
299K ASN
300K MET
301K 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):

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
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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