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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2d29
OXIDOREDUCTASE HEADER
STRUCTURAL STUDY ON PROJECT ID TT0172 FROM THERMUS THERMOPHILUS HB8 TITLE
ACYL-COA 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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FAD B1001
87A LEU
95A LEU
125A TRP
127A LEU
128A THR
129A GLU
132A SER
133A GLY
134A SER
135A ASP
157A GLN
158A PHE
159A ILE
160A THR
207A LYS
215A THR
270E TYR
274E ARG
276E ALA
277E PHE
281E ILE
284E PHE
285C GLU
286E GLY
287E VAL
289C PHE
290E LYS
342E GLN
343E ILE
344E LEU
345E GLY
346E GLY
347E TYR
349E TYR
350E VAL
364A LEU
367A ILE
368A GLY
369A GLU
370A GLY
371A THR
373A GLU
374A ILE
377A LEU
FAD F1001
87E LEU
91E SER
95E LEU
125E TRP
127E LEU
128E THR
129E GLU
132E SER
133E GLY
134E SER
135E ASP
158E PHE
159E ILE
160E THR
207E LYS
215E THR
270A TYR
274A ARG
276A ALA
277A PHE
281A ILE
284A PHE
285G GLU
286A GLY
287A VAL
289G PHE
290A LYS
342A GLN
343A ILE
344A LEU
345A GLY
346A GLY
347A TYR
349A TYR
350A VAL
364E LEU
367E ILE
368E GLY
369E GLU
370E GLY
371E THR
373E GLU
374E ILE
377E LEU
FAD D2001
87C LEU
95C LEU
125C TRP
127C LEU
128C THR
129C GLU
132C SER
133C GLY
134C SER
135C ASP
157C GLN
158C PHE
159C ILE
160C THR
207C LYS
215C THR
270G TYR
274G ARG
276G ALA
277G PHE
281G ILE
284G PHE
285A GLU
286G GLY
287G VAL
289A PHE
290G LYS
342G GLN
343G ILE
344G LEU
345G GLY
346G GLY
347G TYR
349G TYR
350G VAL
364C LEU
367C ILE
368C GLY
369C GLU
370C GLY
371C THR
373C GLU
374C ILE
377C LEU
FAD H2001
87G LEU
91G SER
95G LEU
125G TRP
127G LEU
128G THR
129G GLU
132G SER
133G GLY
134G SER
135G ASP
158G PHE
159G ILE
160G THR
207G LYS
215G THR
270C TYR
274C ARG
276C ALA
277C PHE
281C ILE
284C PHE
285E GLU
286C GLY
287C VAL
289E PHE
290C LYS
342C GLN
343C ILE
344C LEU
345C GLY
346C GLY
347C TYR
349C TYR
350C VAL
364G LEU
367G ILE
368G GLY
369G GLU
370G GLY
371G THR
373G GLU
374G ILE
377G LEU
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
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.

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apo-structure
pdb ID
1ws9 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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FAD NAME: FLAVIN-ADENINE DINUCLEOTIDE
FORMULA: C27 H33 N9 O15 P2
SMILES: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CC(O)C(O)C(O)COP(O)(=O)OP(O)(=O)OCC4OC(C(O)C4O)[n]5cnc6c(N)ncnc56)c2cc1C
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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