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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3efv
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF A PUTATIVE SUCCINATE-SEMIALDEHYDE DEHYDROGENASE FROM SALMONELLA TYPHIMURIUM LT2 WITH BOUND NAD TITLE
PUTATIVE SUCCINATE-SEMIALDEHYDE 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 D 463
133C ILE
135C PRO
136C TRP
137C ASN
138C PHE
142C GLN
145C ARG
160C LYS
162C ALA
163C PRO
193C ASN
196C VAL
197C SER
210C VAL
211C THR
212C GLY
213C SER
214C VAL
216C ALA
219C ALA
220C ILE
223C GLN
234C GLU
235C LEU
236C GLY
268C CYS
312C ARG
315C LEU
365C GLU
367C PHE
393C LEU
431C PHE
NAD B 463
133A ILE
135A PRO
136A TRP
137A ASN
138A PHE
142A GLN
145A ARG
160A LYS
161A HIS
162A ALA
163A PRO
193A ASN
196A VAL
210A VAL
211A THR
212A GLY
213A SER
215E ARG
216A ALA
219A ALA
220A ILE
223A GLN
234A GLU
235A LEU
236A GLY
268A CYS
312A ARG
315A LEU
365A GLU
367A PHE
393A LEU
431A PHE
NAD F 463
133E ILE
135E PRO
136E TRP
137E ASN
138E PHE
142E GLN
145E ARG
160E LYS
161E HIS
162E ALA
163E PRO
193E ASN
196E VAL
210E VAL
211E THR
212E GLY
213E SER
214E VAL
215E ARG
216E ALA
219E ALA
220E ILE
223E GLN
234E GLU
235E LEU
236E GLY
268E CYS
312E ARG
315E LEU
365E GLU
367E PHE
393E LEU
431E PHE
NAD H 463
133G ILE
135G PRO
136G TRP
137G ASN
138G PHE
142G GLN
145G ARG
160G LYS
161G HIS
162G ALA
163G PRO
193G ASN
196G VAL
197G SER
210G VAL
211G THR
212G GLY
213G SER
214G VAL
215G ARG
216G ALA
219G ALA
220G ILE
223G GLN
234G GLU
235G LEU
236G GLY
268G CYS
312G ARG
315G LEU
365G GLU
367G PHE
393G LEU
431G PHE
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
3etf 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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