university lille north of france LigASite database of binding sites
apo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1e5l
OXIDOREDUCTASE HEADER
APO SACCHAROPINE REDUCTASE FROM MAGNAPORTHE GRISEA TITLE
SACCHAROPINE REDUCTASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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9 LEU
10 GLY
11 SER
12 GLY
13 PHE
14 VAL
15 THR
32 ALA
33 CYS
34 ARG
35 THR
38 SER
54 LEU
55 ASP
56 VAL
57 ASN
74 SER
75 LEU
76 ILE
77 PRO
78 TYR
80 PHE
81 HIS
98 THR
99 SER
100 TYR
124 GLY
125 LEU
126 ASP
127 PRO
155 CYS
156 GLY
157 GLY
170 TYR
174 TRP
175 SER
176 SER
178 GLY
182 ALA
223 ASN
224 ARG
245 THR
247 ARG
395 MET
399 VAL
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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
1e5q NDPF_500 SHRF_501 67 246 Details
NDPA_500 SHRA_501 67 245
NDPH_500 SHRH_501 67 248
NDPD_500 SHRD_501 67 248
NDPC_500 SHRC_501 67 245
NDPB_500 SHRB_501 67 253
NDPE_500 SHRE_501 67 245
NDPG_500 SHRG_501 67 247
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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