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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1pzk
TOXIN HEADER
CHOLERA TOXIN B-PENTAMER COMPLEXED WITH N-ACYL PHENYL GALACTOSIDE 9H 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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J12 J 104
11I GLU
12I TYR
13I HIS
14I ASN
31C LEU
33C GLY
51I GLU
56I GLN
57I HIS
58I ILE
61I GLN
88I TRP
90I ASN
91I LYS
J12 F 106
11E GLU
12E TYR
13E HIS
14E ASN
33G GLY
51E GLU
56E GLN
57E HIS
58E ILE
61E GLN
88E TRP
90E ASN
91E LYS
J12 H 107
11G GLU
12G TYR
13G HIS
14G ASN
33I GLY
51G GLU
56G GLN
57G HIS
58G ILE
61G GLN
88G TRP
90G ASN
91G LYS
J12 D 108
11C GLU
12C TYR
13C HIS
14C ASN
33A GLY
34A LYS
35A ARG
51C GLU
56C GLN
57C HIS
58C ILE
61C GLN
88C TRP
90C ASN
91C 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
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
1jr0 A24E_104 Details
A24O_104
A24B_104
A24L_104
A24H_104
A24Q_104
A24J_104
A24R_104
A24T_104
A24G_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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J12 NAME: N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-(2-THIOPHEN-2-YL-ACETYLAMINO)-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-BENZAMIDE
FORMULA: C29 H43 N5 O8 S1
SMILES: NCCCN1CCN(CCCNC(=O)c2cc(NC(=O)Cc3sccc3)cc(OC4OC(CO)C(O)C(O)C4O)c2)CC1
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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