university lille north of france LigASite database of binding sites
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LigASite v3.0 (nr25) - non-redundant
LigASite v3.0 (redundant) - redundant
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apo-structureHelp

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

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1byi
LIGASE HEADER
STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION TITLE
DETHIOBIOTIN SYNTHASE 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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11 THR
12 GLU
13 VAL
14 GLY
15 LYS
16 THR
17 VAL
37 LYS
40 ALA
41 SER
42 GLY
52 ASN
53 SER
54 ASP
79 PRO
80 THR
81 SER
82 PRO
115 GLU
117 ALA
118 GLY
119 GLY
122 THR
123 PRO
149 LEU
150 GLY
151 CYS
152 ILE
153 ASN
175 ASN
176 ASP
177 VAL
187 TYR
203 ILE
204 PRO
205 TRP
206 LEU
207 ALA
210 PRO
211 GLU
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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
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
1dag ACPB_226 DSDB_225 47 186 Details
ACPA_226 DSDA_225 47 181
1dai DSDB_225 16 85 Details
DSDA_225 16 88
1daf DSDB_225 16 87 Details
ADPB_226 _CAB_227 28 96
ADPA_226 _CAA_227 28 102
DSDA_225 16 87
1dae IKTA_225 16 86 Details
IKTB_225 16 81
1dak ADPD_802 DPPD_801 _MGD_901 _MGD_902 49 195 Details
ADPC_802 DPPC_801 _MGC_902 _MGC_901 49 201
1dad ADPB_225 27 94 Details
ADPA_225 27 95
1dam ADPD_801 PHOD_802 IUMD_901 IUMD_902 CYCD_803 49 189 Details
ADPC_801 IUMC_902 IUMC_901 PHOC_802 CYCC_803 49 192
1dah ACPA_226 _MNA_369 DNNA_225 45 182 Details
ACPB_226 _MNB_369 DNNB_225 45 187
1bs1 ADPD_802 IUMD_901 IUMD_902 DAFD_379 49 193 Details
ADPC_802 IUMC_902 IUMC_901 DAFC_379 49 194
v3.0
January 2008		 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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