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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1jn2
SUGAR BINDING PROTEIN HEADER
CRYSTAL STRUCTURE OF MESO-TETRASULPHONATOPHENYL PORPHYRIN COMPLEXED WITH CONCANAVALIN A TITLE
CONCANAVALIN A 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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SFP D1001
12A TYR
14A ASN
16A ASP
33A ARG
98A GLY
99A LEU
100A TYR
208A ASP
226A THR
227A GLY
228A ARG
229A LEU
SFP P1001
12M TYR
14M ASN
16M ASP
33M ARG
98M GLY
99M LEU
100M TYR
208M ASP
226M THR
227M GLY
228M ARG
229M 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:

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).

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

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apo-structure
pdb ID
1dq0 Details
other holo-structures
pdb ID Ligand Unique ID
1nxd AZIQ_910 AZIR_913 GOLG_812 Details
AZIV_910 AZIW_913 GOLL_812
1tei MANA_243 NAGC_240 MANB_242 MANZ_241 NAGD_244 Details
MANT_241 MANU_243 NAGW_240 MANV_242
MANL_241 NAGO_240 NAGP_244 MANN_242 MANM_243
MANH_241 NAGK_240 MANI_243 MANJ_242
MANB_241 MANC_243 NAGE_240 MAND_242
MAND_241 MANE_243 MANF_242 NAGG_240
MANR_241 MANS_243 NAGU_240 MANT_242
MANJ_241 NAGM_240 MANL_242 NAGN_244 MANK_243
1ona MANP_240 MMAR_241 MANQ_242 Details
MANJ_240 MANK_242 MMAL_241
MAND_240 MMAF_241 MANE_242
MANV_240 MMAX_241 MANW_242
1bxh AMGQ_242 AMGR_241 Details
1cjp MUGL_240 Details
3d4k H1MA_241 MANF_242 MANE_240 Details
H1MG_241 MANK_240 MANL_242
1cvn MANP_240 MANQ_242 MANR_241 Details
MANJ_240 MANL_241 MANK_242
MANV_240 MANX_241 MANW_242
MAND_240 MANF_241 MANE_242
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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SFP NAME: 5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE
FORMULA: C44 H34 N4 O12 S4
SMILES: OS(O)([O-])c1ccc(cc1)C2=C3NC(=C(c4ccc(cc4)S(O)(O)[O-])C5=NC(=C(c6[nH]c(cc6)C(=C7C=CC2=N7)c8ccc(cc8)S(O)(O)[O-])c9ccc(cc9)S(O)(O)[O-])C=C5)C=C3
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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