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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2yzg
LIGASE HEADER
CRYSTAL STRUCTURE OF D-ALA:D-ALA LIGASE FROM THERMUS THERMOPHILUS HB8 TITLE
D-ALANINE--D-ALANINE LIGASE 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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13 GLU
16 VAL
82 HIS
87 GLU
113 CYS
114 MET
116 LYS
131 VAL
151 PHE
153 LYS
154 PRO
155 ALA
156 ASN
157 THR
158 GLY
159 SER
160 SER
163 ILE
165 ARG
189 GLU
190 LYS
191 ALA
192 LEU
195 VAL
197 GLU
199 GLU
217 ARG
218 TYR
219 GLU
220 ALA
221 PRO
222 PHE
223 TYR
228 LYS
229 TYR
268 ARG
270 ASP
272 PHE
281 ASN
282 GLU
284 ASN
286 ILE
287 PRO
288 GLY
292 THR
293 SER
294 MET
295 TYR
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
2zdq ATPD1502 DALC_403 DALC_404 42 194 Details
ATPB1501 DALA_401 DALA_402 42 186
2zdh ADPN_704 _MGO_817 28 115 Details
ADPF_702 _MGH_813 28 102
ADPB_701 _MGC_811 _MGD_812 29 117
ADPJ_703 _MGL_815 28 113
2zdg ADPI_404 _MGJ_602 28 106 Details
ADPD_402 27 106
ADPF_403 _MGG_601 28 115
ADPB_401 27 96
2yzn ANPD_402 31 126 Details
ANPH_403 31 111
ANPF_403 31 113
ANPJ_401 31 107
ANPL_402 31 128
ANPB_401 31 109
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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