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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20 GLU
29 LYS
31 GLU
42 ASP
43 ARG
51 TYR
55 TYR
56 GLY
57 TYR
63 SER
65 ASP
67 ASP
68 PRO
69 VAL
70 ASP
95 MET
97 ASP
98 GLU
99 ALA
102 ASP
104 LYS
138 PHE
141 TYR
142 LYS
148 LYS
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
2au8 PO4P_180 _MNS_201 _MNT_204 _MNQ_203 _CLO_208 _MNR_202 10 73 Details
PO4T_180 _MNU_203 _MNW_201 _CLS_208 _MNX_204 _MNV_202 10 73
2au6 POPT_182 _MNS_203 __FX_211 _MNV_201 _MNU_202 13 71 Details
POPP_182 _MNQ_202 _MNR_201 __FT_211 _MNO_203 13 71
POPH_182 _MNG_203 _MNI_202 __FL_211 _MNJ_201 13 71
POPR_182 _MNQ_203 _MNS_202 _MNT_201 __FV_211 13 71
POPF_182 _MNG_202 _MNH_201 __FJ_211 _MNE_203 13 71
POPD_182 __FH_211 _MNE_202 _MNC_203 _MNF_201 13 71
1i6t POPD_411 _CAZ_302 _CAB_303 _CAA_301 12 78 Details
POPX_411 _CAV_303 _CAU_301 _CAT_302 12 78
POPT_411 _CAP_302 _CAR_303 _CAQ_301 12 78
POPJ_411 _CAH_303 _CAG_301 _CAF_302 12 73
POPH_411 _CAF_303 _CAE_301 _CAD_302 12 73
POPN_411 _CAL_303 _CAK_301 _CAJ_302 12 78
2auu POPG_180 _MGE_201 __FH_211 _MGF_204 _MGC_202 _MGD_203 14 76 Details
POPI_180 __FJ_211 _MGE_202 _MGH_204 _MGG_201 _MGF_203 14 76
POPW_180 _MGV_204 _MGS_202 __FX_211 _MGT_203 _MGU_201 14 79
POPC_180 _MGZ_203 _MGY_202 __FD_211 _MGB_204 _MGA_201 14 80
POPS_180 _MGP_203 __FT_211 _MGQ_201 _MGO_202 _MGR_204 14 79
POPM_180 __FN_211 _MGK_201 _MGI_202 _MGJ_203 _MGL_204 14 80
2au9 POPS_180 _MNU_204 _MNQ_203 _MNT_201 _MNR_202 _CLP_208 __FV_211 15 84 Details
POPH_180 _MNI_201 _CLE_208 _MNG_202 _MNJ_204 __FK_211 _MNF_203 15 81
POPO_180 _MNM_203 _MNQ_204 _MNP_201 _MNN_202 _CLL_208 __FR_211 15 80
POPK_180 _MNI_203 _CLH_208 _MNL_201 _MNJ_202 __FN_211 _MNM_204 15 81
POPD_180 _MNC_202 _MNE_201 _CLA_208 _MNF_204 _MNB_203 __FG_211 15 80
POPZ_180 _CLW_208 _MNB_204 __FC_211 _MNX_203 _MNA_201 _MNY_202 15 84
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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