university lille north of france LigASite database of binding sites
holo-structureHelp

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

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1dam
LIGASE HEADER
DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM TITLE
PROTEIN (DETHIOBIOTIN SYNTHETASE) COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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PO4 C 802
11A THR
15A LYS
37A LYS
41A SER
54A ASP
115A GLU
117A ALA
118A GLY
MG E 902
11A THR
12A GLU
54A ASP
DTB F 803
11A THR
40A ALA
41A SER
42A GLY
52A ASN
54A ASP
79A PRO
80A THR
81A SER
82A PRO
117A ALA
118A GLY
119A GLY
122A THR
123A PRO
149G LEU
150G GLY
152G ILE
153G ASN
187G TYR
PO4 I 802
11G THR
15G LYS
37G LYS
41G SER
54G ASP
115G GLU
117G ALA
118G GLY
MG K 902
11G THR
12G GLU
54G ASP
DTB L 803
11G THR
41G SER
42G GLY
52G ASN
54G ASP
79G PRO
80G THR
81G SER
82G PRO
117G ALA
118G GLY
119G GLY
122G THR
123G PRO
149A LEU
150A GLY
152A ILE
153A ASN
187A TYR
ADP B 801
12A GLU
13A VAL
14A GLY
15A LYS
16A THR
17A VAL
54A ASP
115A GLU
175A ASN
176A ASP
177A VAL
203A ILE
204A PRO
205A TRP
206A LEU
207A ALA
210A PRO
211A GLU
ADP H 801
12G GLU
13G VAL
14G GLY
15G LYS
16G THR
17G VAL
54G ASP
115G GLU
175G ASN
176G ASP
177G VAL
203G ILE
204G PRO
205G TRP
206G LEU
207G ALA
210G PRO
211G GLU
MG D 901
16A THR
54A ASP
115A GLU
MG J 901
16G THR
54G ASP
115G 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:

LigPlot (hosted at the EBI):

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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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

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apo-structure
pdb ID
1byi Details
other holo-structures
pdb ID Ligand Unique ID
1dai DSDB_225 Details
DSDA_225
1dad ADPD_225 Details
ADPB_225
1bs1 ADPB_802 DAAC_850 _MGE_902 _MGD_901 Details
ADPG_802 DAAH_850 _MGJ_902 _MGI_901
1dag ACPD_226 DSDC_225 Details
ACPB_226 DSDA_225
1a82 ATPF_802 _MGG_901 DNNH_801 Details
ATPB_802 _MGC_901 DNND_801
1daf DSDD_225 Details
ADPB_226 _CAC_227
DSDA_225
ADPE_226 _CAF_227
1dak ADPB_802 DPUC_801 _MGE_901 _MGF_902 Details
ADPH_802 DPUI_801 _MGK_901 _MGL_902
1dae IKTB_225 Details
IKTD_225
1dah ACPB_226 DNNH_225 _MNC_369 Details
ACPF_226 _MNG_369 DNND_225
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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ADP NAME: ADENOSINE-5'-DIPHOSPHATE
FORMULA: C10 H15 N5 O10 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
PO4 NAME: PHOSPHATE ION
FORMULA: O4 P1
SMILES: [O-]P([O-])([O-])=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
DTB NAME: 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID
FORMULA: C10 H18 N2 O3
SMILES: CC1NC(=O)NC1CCCCCC(O)=O
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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