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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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:

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
1dai DSDB_225 16 85 Details
DSDA_225 16 88
1dad ADPD_225 27 94 Details
ADPB_225 27 95
1bs1 ADPB_802 DAAC_850 _MGE_902 _MGD_901 49 194 Details
ADPG_802 DAAH_850 _MGJ_902 _MGI_901 49 194
1dag ACPD_226 DSDC_225 47 186 Details
ACPB_226 DSDA_225 47 181
1a82 ATPF_802 _MGG_901 DNNH_801 45 184 Details
ATPB_802 _MGC_901 DNND_801 45 187
1dam ADPB_801 PO4C_802 _MGE_902 _MGD_901 DTBF_803 49 192 Details
ADPH_801 PO4I_802 _MGK_902 DTBL_803 _MGJ_901 49 189
1daf DSDD_225 16 87 Details
ADPB_226 _CAC_227 28 102
DSDA_225 16 87
ADPE_226 _CAF_227 28 96
1dak ADPB_802 DPUC_801 _MGE_901 _MGF_902 49 201 Details
ADPH_802 DPUI_801 _MGK_901 _MGL_902 49 195
1dae IKTB_225 16 81 Details
IKTD_225 16 86
1dah ACPB_226 DNNH_225 _MNC_369 45 182 Details
ACPF_226 _MNG_369 DNND_225 45 187
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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