university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (redundant) - redundant
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holo-structureHelp

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

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1tei
LECTIN HEADER
STRUCTURE OF CONCANAVALIN A COMPLEXED TO BETA-D-GLCNAC (1, 2)ALPHA-D-MAN-(1,6)[BETA-D-GLCNAC(1,2)ALPHA-D-MAN (1,6) ]ALPHA-D-MAN 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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MAN B 242
12B TYR
14B ASN
16B ASP
99B LEU
100B TYR
228B ARG
MAN C 242
12C TYR
14C ASN
16C ASP
99C LEU
100C TYR
228C ARG
MAN A 242
12A TYR
14A ASN
16A ASP
99A LEU
100A TYR
228A ARG
MAN D 242
12D TYR
14D ASN
16D ASP
99D LEU
100D TYR
228D ARG
MAN A 241
12A TYR
14A ASN
98A GLY
99A LEU
100A TYR
207A ALA
208A ASP
227A GLY
228A ARG
MAN A 243
12A TYR
13A PRO
14A ASN
15A THR
16A ASP
NAG A 244
12A TYR
13A PRO
21A SER
205A HIS
MAN D 241
12D TYR
14D ASN
98D GLY
99D LEU
100D TYR
207D ALA
208D ASP
227D GLY
228D ARG
MAN D 243
12D TYR
13D PRO
14D ASN
15D THR
16D ASP
NAG D 244
12D TYR
13D PRO
21D SER
205D HIS
MAN C 241
12C TYR
14C ASN
98C GLY
99C LEU
100C TYR
207C ALA
208C ASP
227C GLY
228C ARG
MAN C 243
12C TYR
13C PRO
14C ASN
15C THR
16C ASP
NAG C 244
12C TYR
13C PRO
21C SER
205C HIS
MAN B 241
12B TYR
14B ASN
98B GLY
99B LEU
100B TYR
207B ALA
208B ASP
227B GLY
228B ARG
MAN B 243
12B TYR
13B PRO
14B ASN
15B THR
16B ASP
NAG B 244
12B TYR
13B PRO
21B SER
205B HIS
NAG A 240
98A GLY
99A LEU
168A SER
224A GLY
226A THR
227A GLY
228A ARG
229A LEU
NAG D 240
98D GLY
99D LEU
168D SER
224D GLY
226D THR
227D GLY
228D ARG
229D LEU
NAG C 240
98C GLY
99C LEU
168C SER
224C GLY
226C THR
227C GLY
228C ARG
229C LEU
NAG B 240
98B GLY
99B LEU
168B SER
224B GLY
226B THR
227B GLY
228B ARG
229B 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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

» NAG-MAN-MAN-MAN-
NAG 		» Jmol
» CA » Jmol
» MN » Jmol
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
Hide table of related structures
Help

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
1ona MANB_240 MMAB_241 MANB_242 Details
MANC_240 MMAC_241 MANC_242
MANA_240 MANA_242 MMAA_241
MAND_240 MMAD_241 MAND_242
1cjp MUGC_240 Details
1bxh AMGD_241 AMGD_242 Details
1jn2 SFPD1001 Details
SFPG1001
1cvn MANA_240 MANA_241 MANA_242 Details
MANC_240 MANC_241 MANC_242
MAND_240 MAND_241 MAND_242
MANB_240 MANB_242 MANB_241
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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MAN NAME: ALPHA-D-MANNOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
NAG NAME: N-ACETYL-D-GLUCOSAMINE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
v6.0
October 2008		 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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