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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1daf
LIGASE HEADER
DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8- AMINO-NONANOIC ACID, ADP, AND CALCIUM TITLE
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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DSD A 225
11A THR
12A GLU
15A LYS
37A LYS
40A ALA
41A SER
52A ASN
54A ASP
79A PRO
80A THR
81A SER
82A PRO
117A ALA
118A GLY
119A GLY
122A THR
123A PRO
149D LEU
150D GLY
152D ILE
153D ASN
187D TYR
DSD D 225
11D THR
12D GLU
15D LYS
37D LYS
40D ALA
41D SER
52D ASN
54D ASP
79D PRO
80D THR
81D SER
82D PRO
117D ALA
118D GLY
119D GLY
122D THR
123D PRO
149A LEU
150A GLY
152A ILE
153A ASN
187A TYR
ADP B 226
11A THR
12A GLU
13A VAL
14A GLY
15A LYS
16A THR
17A VAL
37A LYS
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 E 226
11D THR
12D GLU
13D VAL
14D GLY
15D LYS
16D THR
17D VAL
37D LYS
54D ASP
115D GLU
175D ASN
176D ASP
177D VAL
203D ILE
204D PRO
205D TRP
206D LEU
207D ALA
210D PRO
211D GLU
CA C 227
12A GLU
53A SER
54A ASP
CA F 227
12D GLU
53D SER
54D ASP
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
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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
1dam ADPB_801 PO4C_802 _MGE_902 _MGD_901 DTBF_803 Details
ADPH_801 PO4I_802 _MGK_902 DTBL_803 _MGJ_901
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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DSD NAME: 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID
FORMULA: C10 H20 N2 O4
SMILES: CC(N)C(CCCCCC(O)=O)NC(O)=O
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
CA NAME: CALCIUM ION
FORMULA: CA1
SMILES: [Ca++]
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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