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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1xlt
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF TRANSHYDROGENASE [(DOMAIN I)2:DOMAIN III] HETEROTRIMER COMPLEX TITLE
NAD(P) TRANSHYDROGENASE SUBUNIT ALPHA PART 1 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 C 400
125A MET
126A PRO
127A ARG
128A ILE
129A SER
131A ALA
132A GLN
135A ASP
138A SER
141A SER
179A GLY
180A VAL
181A GLY
182A VAL
183A ALA
201A THR
202A ASP
203A VAL
204A ARG
210A GLN
244A ARG
264A THR
265A ALA
266A LEU
267A ILE
268A PRO
273A PRO
274A VAL
275A LEU
NAD E 400
127D ARG
137D LEU
138D SER
141D SER
179D GLY
180D VAL
181D GLY
182D VAL
183D ALA
202D ASP
203D VAL
204D ARG
264D THR
265D ALA
266D LEU
267D ILE
268D PRO
273D PRO
275D LEU
NDP I 500
129D SER
132D GLN
182D VAL
209D GLU
210D GLN
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
1l7d Details
other holo-structures
pdb ID Ligand Unique ID
1u2g APRB_500 Details
APRD_600 NDPG_400
1hzz NAPE_300 Details
NADB_400
1u28 NADB_500 Details
NAPH_400
NADD_600
2oo5 NAPJ_400 TXDH_600 Details
TXDD_500
1f8g NADB2501 Details
NADD2503
2oor NADB_500 Details
TXPG_400
NADD_600
1l7e NAIB_701 Details
1u2d NADB_500 Details
NADD_600 NDPG_400
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
NDP NAME: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H30 N7 O17 P3
SMILES: NC(=O)C1=CN(C=CC1)C2OC(COP(O)(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=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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