university lille north of france LigASite database of binding sites

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

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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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12 TYR
13 PRO
14 ASN
15 THR
16 ASP
21 SER
33 ARG
54 TYR
88 TRP
97 THR
98 GLY
99 LEU
100 TYR
113 SER
114 LYS
115 LEU
124 ASN
125 ALA
126 LEU
128 PHE
129 MET
130 PHE
134 SER
137 GLN
139 ASP
141 ILE
143 GLN
167 GLY
168 SER
176 TYR
178 PRO
179 VAL
180 HIS
181 ILE
183 GLU
189 ALA
190 SER
191 PHE
205 HIS
207 ALA
208 ASP
224 GLY
226 THR
227 GLY
228 ARG
229 LEU
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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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
1nxd AZIQ_910 AZIR_913 GOLG_812 12 91 Details
AZIV_910 AZIW_913 GOLL_812 12 92
1tei MANA_243 NAGC_240 MANB_242 MANZ_241 NAGD_244 62 151 Details
MANT_241 MANU_243 NAGW_240 MANV_242 48 121
MANL_241 NAGO_240 NAGP_244 MANN_242 MANM_243 62 136
MANH_241 NAGK_240 MANI_243 MANJ_242 48 112
MANB_241 MANC_243 NAGE_240 MAND_242 48 110
MAND_241 MANE_243 MANF_242 NAGG_240 48 117
MANR_241 MANS_243 NAGU_240 MANT_242 48 126
MANJ_241 NAGM_240 MANL_242 NAGN_244 MANK_243 62 138
1jn2 SFPD1001 33 72 Details
SFPP1001 33 72
1ona MANP_240 MMAR_241 MANQ_242 35 85 Details
MANJ_240 MANK_242 MMAL_241 35 89
MAND_240 MMAF_241 MANE_242 35 85
MANV_240 MMAX_241 MANW_242 35 89
1bxh AMGQ_242 AMGR_241 24 73 Details
1cjp MUGL_240 24 70 Details
3d4k H1MA_241 MANF_242 MANE_240 37 80 Details
H1MG_241 MANK_240 MANL_242 37 84
1cvn MANP_240 MANQ_242 MANR_241 34 81 Details
MANJ_240 MANL_241 MANK_242 34 91
MANV_240 MANX_241 MANW_242 34 88
MAND_240 MANF_241 MANE_242 34 86
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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