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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1m1z
HYDROLASE HEADER
BETA-LACTAM SYNTHETASE APO ENZYME TITLE
BETA-LACTAM SYNTHETASE 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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247 VAL
248 LEU
249 SER
251 GLY
252 ILE
253 ASP
254 SER
271 VAL
272 SER
273 MET
274 GLY
275 THR
277 THR
278 SER
279 ASN
280 GLU
305 LEU
320 ASP
322 ASP
323 ILE
326 TYR
329 PRO
330 LEU
333 LEU
346 THR
347 GLY
348 TYR
349 GLY
350 ALA
351 ASP
352 ILE
357 MET
358 HIS
373 ASP
376 THR
377 PHE
380 LEU
382 GLU
423 LYS
427 ARG
441 ARG
442 PRO
443 LYS
444 LEU
445 GLY
446 VAL
447 HIS
449 GLY
450 SER
455 SER
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
1mbz GOLL_605 POPI_604 IOTH_603 _MGK_602 _MGJ_601 55 220 Details
GOLF_607 IOTB_606 _MGE_604 POPD_605 _MGC_603 55 239
POPI_604 IOTH_603 _MGK_602 _MGJ_601 49 191
1mb9 ATPB_701 _MGD_604 _MGC_603 33 126 Details
ATPH_702 _MGI_602 _MGJ_601 33 125
1mc1 AMPH_705 PCXL_706 _MGI_602 POPJ_704 _MGK_605 50 193 Details
AMPB_702 POPC_701 _MGD_603 _MGE_601 PCXF_703 50 215
1jgt APCB_801 CMAA_803 _MGC_902 49 192 Details
APCE_802 _MGF_901 CMAD_804 49 193
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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