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 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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3M1 D 128
106G THR
108G ALA
109C ALA
110C LEU
117C SER
118C THR
119C THR
121G VAL
3M1 H 128
106C THR
108C ALA
109G ALA
110G LEU
117G SER
118G THR
119G THR
121C VAL
3M1 B 128
106E THR
108E ALA
109A ALA
110A LEU
117A SER
118A THR
119E THR
121E VAL
3M1 F 128
106A THR
108A ALA
109E ALA
110E LEU
117E SER
118E THR
119A THR
121A VAL
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

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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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pdb ID
1bmz Details
other holo-structures
pdb ID Ligand Unique ID
2f7i 26CD_325 26CH_325 Details
26CB_326 26CF_326
1y1d FHIB2000 FHIF2000 Details
FHID3000 FHIH3000
1tz8 DESJ_128 Details
1e5a TBPB_999 TBPF_999 Details
TBPD_998 TBPH_998
3ipb JZDA_128 Details
2qgd MR5D_201 MR5H_201 Details
MR5B_200 MR5F_200
1tt6 DESB_128 DESG_128 Details
DESK_129 DESL_129
3ipe JZEB_128 Details
1e4h PBRF_998 PBRL_998 Details
PBRC_999 PBRI_999
3b56 DIUB2000 DIUF2000 Details
DIUD3000 DIUH3000
2fbr 44CB_173 44CE_173 Details
2b15 DNFC_130 DNFI_130 Details
DNFF_128 DNFL_128
2roy P28B_128 P28F_128 Details
P28D_128 P28H_128
2f8i 205D1001 205H1001 Details
205B1002 205F1002
2qge MR6D_200 MR6H_200 Details
MR6B_201 MR6F_201
2g9k NE1D_500 NE1H_500 Details
NE1B_501 NE1F_501
2qgc MR4D_128 MR4H_128 Details
MR4B_128 MR4F_128
2rox T44E_128 T44J_128 Details
T44C_128 T44H_128
1z7j T4AD_129 T4AH_129 Details
3cn3 LJ4A_128 LJ4C_128 Details
LJ4B_128 LJ4D_128
2b77 3CAD_239 3CAH_239 Details
3CAB_240 3CAF_240
1tyr READ_130 REAH_130 Details
REAB_131 REAF_131
1u21 P2CC_211 P2CD_211 Details
P2CG_221 P2CH_221
3d2t 1FLB_502 1FLF_502 Details
1FLD_500 1FLH_500
3p3u 3M4D_128 3M4H_128 Details
3M4B_128 3M4F_128
2gab NE2G_502 NE2H_502 Details
NE2C_501 NE2D_501
3hj0 A93B_128 A93D_128 Details
A93A_128 A93C_128
3gs4 7BDB_500 7BDD_500 Details
7BDA_501 7BDC_501
2flm 6CAB_201 6CAE_201 Details
3kgu GEND3071 GENH3071 Details
GENB3071 GENF3071
2g5u PCQC_240 PCQD_240 Details
3p3t 3M3D_128 3M3H_128 Details
3M3B_128 3M3F_128
3p3s 3M2B_128 3M2H_128 Details
3M2E_128 3M2K_128
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

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3M1 NAME: not_found
FORMULA: not_found
SMILES: not_found
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
Script execution time: 6.122 seconds