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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1jr0
TOXIN HEADER
CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0011 TITLE
CHOLERA TOXIN B SUBUNIT 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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A24 H 104
11D GLU
12D TYR
13D HIS
14D ASN
33F GLY
34F LYS
35F ARG
51D GLU
56D GLN
57D HIS
58D ILE
61D GLN
88D TRP
90D ASN
91D LYS
A24 Q 104
11P GLU
12P TYR
13P HIS
14P ASN
33S GLY
34S LYS
51P GLU
56P GLN
57P HIS
58P ILE
61P GLN
88P TRP
90P ASN
91P LYS
A24 R 104
11N GLU
12N TYR
13N HIS
14N ASN
33P GLY
34P LYS
35P ARG
51N GLU
56N GLN
57N HIS
58N ILE
61N GLN
88N TRP
90N ASN
91N LYS
A24 G 104
11F GLU
12F TYR
13F HIS
14F ASN
33I GLY
34I LYS
51F GLU
56F GLN
57F HIS
58F ILE
61F GLN
88F TRP
90F ASN
91F LYS
A24 E 104
12M TYR
13M HIS
14M ASN
33N GLY
34N LYS
51M GLU
55M SER
56M GLN
57M HIS
58M ILE
59D ASP
60D SER
61M GLN
88M TRP
90M ASN
91M LYS
A24 O 104
12C TYR
13C HIS
14C ASN
33D GLY
34D LYS
51C GLU
55C SER
56C GLN
57C HIS
58C ILE
59N ASP
60N SER
61C GLN
88C TRP
90C ASN
91C LYS
A24 B 104
12I TYR
13I HIS
14I ASN
33A GLY
34A LYS
51I GLU
55I SER
56I GLN
57I HIS
58I ILE
61I GLN
88I TRP
90I ASN
91I LYS
A24 L 104
12S TYR
13S HIS
14S ASN
33K GLY
34K LYS
51S GLU
55S SER
56S GLN
57S HIS
58S ILE
61S GLN
88S TRP
90S ASN
91S LYS
A24 J 104
12K TYR
13K HIS
14K ASN
33M GLY
34M LYS
51K GLU
56K GLN
57I HIS
58K ILE
59I ASP
60I SER
61K GLN
88K TRP
90K ASN
91K LYS
A24 T 104
12A TYR
13A HIS
14A ASN
33C GLY
34C LYS
51A GLU
56A GLN
57S HIS
58A ILE
59S ASP
60S SER
61A GLN
88A TRP
90A ASN
91A 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:

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
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
1fgb Details
other holo-structures
pdb ID Ligand Unique ID
1rd9 BV2D_105 Details
BV2F_106
BV2I_108
BV2B_104
1pzj J15J_106 Details
J15H_105
1eei GAAH_506 Details
GAAD_508
GAAJ_507
GAAB_504
1pzk J12J_104 Details
J12F_106
J12H_107
J12D_108
1md2 233F2201 233G2203 _SQV2202 Details
233R2201 233S2203 _SQW2202
233T1204 _SQY1205 233U1206
233M1207 CYNO1208 233N1207
233H1204 233I1206 _SQX1205
1rdp BV3L_108 Details
BV3J_107
BV3B_104
BV3G_106
1rcv BV1B_104 Details
BV1J_105
1llr FNGN_104 LNQO_105 Details
FNGK_104 LNQL_105
FNGE_104 LNQF_105
FNGH_104 LNQI_105
FNGB_104 LNQC_105
1rf2 BV4L_108 Details
BV4J_107
BV4G_106
BV4B_104
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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A24 NAME: (3-NITRO-5-(2-MORPHOLIN-4-YL-ETHYLAMINOCARBONYL)PHENYL)-GALACTOPYRANOSIDE
FORMULA: C19 H27 N3 O10
SMILES: OCC1OC(Oc2cc(cc(c2)[N+]([O-])=O)C(=O)NCCN3CCOCC3)C(O)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
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