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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1cd5
ISOMERASE HEADER
GLUCOSAMINE-6-PHOSPHATE DEAMINASE FROM E.COLI, T CONFORMER TITLE
PROTEIN (GLUCOSAMINE 6-PHOSPHATE DEAMINASE) 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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1 MET
2 ARG
40 PRO
41 THR
42 GLY
43 GLY
44 THR
45 PRO
70 ASN
71 MET
72 ASP
85 TYR
137 GLY
138 VAL
139 GLY
140 ASN
141 ASP
143 HIS
144 ILE
145 ALA
146 PHE
150 ALA
151 SER
152 SER
155 SER
158 ARG
159 ILE
160 LYS
161 THR
165 ASP
166 THR
169 ALA
170 ASN
172 ARG
173 PHE
184 TYR
208 LYS
233 PRO
234 LYS
235 ALA
258 LEU
259 GLU
341 THR
342 GLY
343 GLY
344 THR
345 PRO
385 TYR
437 GLY
438 VAL
439 GLY
440 ASN
441 ASP
443 HIS
445 ALA
446 PHE
465 ASP
466 THR
469 ALA
470 ASN
472 ARG
473 PHE
508 LYS
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
2wu1 FGSK1568 19 92 Details
FGSI1568 19 88
FGSC1268 19 100
FGSG1568 19 91
FGSA1268 19 95
FGSE1268 19 93
1fqo FPCH1268 16 82 Details
FPCE1268 16 83
F6RK2268 16 85
F6RN2268 16 85
FPCB1268 16 82
F6RQ2268 16 87
1hor AGPN_268 16 83 Details
AGPB_268 16 75
AGPQ_268 16 82
AGPK_268 16 81
AGPH_268 16 71
1fs5 16GE1267 19 70 Details
16GB1267 19 72
16GH1267 19 70
16GO2267 19 72
1frz 16GF1267 19 70 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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