university lille north of france LigASite database of binding sites
Home
News
Introduction
Methods
Flow Chart
References
Download
About
FAQ
Search
LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
(click to remove window)
Browse dataset
holo-structureHelp

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

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
MAN A 243
12W TYR
13W PRO
14W ASN
15W THR
16W ASP
MAN B 242
12W TYR
14W ASN
16W ASP
99W LEU
100W TYR
228W ARG
MAN Z 241
12W TYR
14W ASN
98W GLY
99W LEU
100W TYR
207W ALA
208W ASP
227W GLY
228W ARG
NAG D 244
12W TYR
13W PRO
205W HIS
MAN T 241
12Q TYR
14Q ASN
98Q GLY
99Q LEU
100Q TYR
207Q ALA
208Q ASP
227Q GLY
228Q ARG
MAN U 243
12Q TYR
13Q PRO
14Q ASN
15Q THR
16Q ASP
MAN V 242
12Q TYR
14Q ASN
16Q ASP
99Q LEU
100Q TYR
228Q ARG
MAN L 241
12I TYR
14I ASN
98I GLY
99I LEU
100I TYR
207I ALA
208I ASP
227I GLY
228I ARG
NAG P 244
12I TYR
13I PRO
21I SER
205I HIS
MAN N 242
12I TYR
14I ASN
16I ASP
99I LEU
100I TYR
228I ARG
MAN M 243
12I TYR
13I PRO
14I ASN
15I THR
16I ASP
MAN H 241
12E TYR
14E ASN
98E GLY
99E LEU
100E TYR
207E ALA
208E ASP
227E GLY
228E ARG
MAN I 243
12E TYR
13E PRO
14E ASN
15E THR
16E ASP
MAN J 242
12E TYR
14E ASN
16E ASP
99E LEU
100E TYR
228E ARG
MAN B 241
12Y TYR
14Y ASN
98Y GLY
99Y LEU
100Y TYR
207Y ALA
208Y ASP
227Y GLY
228Y ARG
MAN C 243
12Y TYR
13Y PRO
14Y ASN
15Y THR
16Y ASP
MAN D 242
12Y TYR
14Y ASN
16Y ASP
99Y LEU
100Y TYR
228Y ARG
MAN D 241
12A TYR
14A ASN
98A GLY
99A LEU
100A TYR
207A ALA
208A ASP
227A GLY
228A ARG
MAN E 243
12A TYR
13A PRO
14A ASN
15A THR
16A ASP
MAN F 242
12A TYR
14A ASN
16A ASP
99A LEU
100A TYR
228A ARG
MAN R 241
12O TYR
14O ASN
98O GLY
99O LEU
100O TYR
207O ALA
208O ASP
227O GLY
228O ARG
MAN S 243
12O TYR
13O PRO
14O ASN
15O THR
16O ASP
MAN T 242
12O TYR
14O ASN
16O ASP
99O LEU
100O TYR
228O ARG
MAN J 241
12G TYR
14G ASN
98G GLY
99G LEU
100G TYR
207G ALA
208G ASP
227G GLY
228G ARG
MAN L 242
12G TYR
14G ASN
16G ASP
99G LEU
100G TYR
228G ARG
NAG N 244
12G TYR
13G PRO
21G SER
205G HIS
MAN K 243
12G TYR
13G PRO
14G ASN
15G THR
16G ASP
NAG C 240
97W THR
98W GLY
99W LEU
141I ILE
143I GLN
168W SER
176I TYR
224W GLY
226W THR
227W GLY
228W ARG
229W LEU
NAG U 240
97O THR
98O GLY
99O LEU
167O GLY
168O SER
224O GLY
226O THR
227O GLY
228O ARG
229O LEU
NAG W 240
98Q GLY
99Q LEU
168Q SER
224Q GLY
226Q THR
227Q GLY
228Q ARG
229Q LEU
NAG O 240
98I GLY
99I LEU
168I SER
224I GLY
226I THR
227I GLY
228I ARG
229I LEU
NAG K 240
98E GLY
99E LEU
168E SER
224E GLY
226E THR
227E GLY
228E ARG
229E LEU
NAG E 240
98Y GLY
99Y LEU
168Y SER
224Y GLY
226Y THR
227Y GLY
228Y ARG
229Y LEU
NAG G 240
98A GLY
99A LEU
168A SER
224A GLY
226A THR
227A GLY
228A ARG
229A LEU
NAG M 240
98G GLY
99G LEU
168G SER
224G GLY
226G THR
227G GLY
228G ARG
229G 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.

(click anywhere in this window to remove it)

Links to external databases:

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

LigPlot (hosted at the EBI):

no entry
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.

(click anywhere in this window to remove it)
» 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.

(click anywhere in this window to remove it)
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
1jn2 SFPD1001 Details
SFPP1001
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.

(click anywhere in this window to remove it)
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
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
Script execution time: 1.1168 seconds