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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1omp
PERIPLASMIC BINDING PROTEIN HEADER
CRYSTALLOGRAPHIC EVIDENCE OF A LARGE LIGAND-INDUCED HINGE- TWIST MOTION BETWEEN THE TWO DOMAINS OF THE MALTODEXTRIN- BINDING PROTEIN INVOLVED IN ACTIVE TRANSPORT AND CHEMOTAXIS TITLE
D-MALTODEXTRIN BINDING PROTEIN 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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12 ASN
14 ASP
15 LYS
42 LYS
44 GLU
45 GLU
62 TRP
63 ALA
65 ASP
66 ARG
111 GLU
150 ASN
153 GLU
154 PRO
155 TYR
156 PHE
210 TYR
230 TRP
260 GLY
262 LEU
330 MET
337 SER
340 TRP
341 TYR
344 ARG
1014 ASP
1015 LYS
1065 ASP
1111 GLU
1150 ASN
1153 GLU
1154 PRO
1155 TYR
1156 PHE
1210 TYR
1230 TRP
1330 MET
1337 SER
1340 TRP
1341 TYR
1344 ARG
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
1dmb BCDB_371 77 124 Details
4mbp GLCA_371 GLCA_372 GLCA_373 GLCA_374 45 162 Details
1ez9 GLCA_381 GLOA_380 GLCA_382 GLCA_383 45 118 Details
GLCB1381 GLCB1382 GLCB1383 GLOB1380 45 115
3mbp GLCA_371 GLCA_372 GLCA_373 34 142 Details
1anf GLCA_371 GLCA_372 23 98 Details
2r6g ATPB1002 31 116 Details
MALG3001 23 82
ATPD1001 31 131
1jw5 GLCA1001 GLCA1002 23 75 Details
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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