university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

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

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1md2
TOXIN HEADER
CHOLERA TOXIN B-PENTAMER WITH DECAVALENT LIGAND BMSC-0013 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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233 T1204
13B HIS
14B ASN
33C GLY
51B GLU
55Q SER
56B GLN
57B HIS
61B GLN
88B TRP
90B ASN
91B LYS
233 H1204
13K HIS
14K ASN
33L GLY
51K GLU
55E SER
56K GLN
57K HIS
61K GLN
88K TRP
90K ASN
91K LYS
233 F2201
14J ASN
33K GLY
34K LYS
51J GLU
55J SER
56J GLN
57D HIS
58D ILE
59D ASP
60D SER
61J GLN
88J TRP
90J ASN
91J LYS
233 G2203
14D ASN
33A GLY
51D GLU
55D SER
56D GLN
57D HIS
58D ILE
61D GLN
88D TRP
90D ASN
91D LYS
233 R2201
14A ASN
33B GLY
34B LYS
51A GLU
55A SER
56A GLN
57P HIS
58P ILE
59P ASP
60P SER
61A GLN
88A TRP
90A ASN
91A LYS
233 S2203
14P ASN
33J GLY
51P GLU
55P SER
56P GLN
57P HIS
58P ILE
61P GLN
88P TRP
90P ASN
91P LYS
233 U1206
14Q ASN
33P GLY
51Q GLU
55Q SER
56Q GLN
57Q HIS
58Q ILE
61Q GLN
88Q TRP
90Q ASN
91Q LYS
233 M1207
14C ASN
33E GLY
51C GLU
55C SER
56C GLN
57C HIS
61C GLN
88C TRP
90C ASN
91C LYS
233 N1207
14L ASN
33Q GLY
51L GLU
55L SER
56L GLN
57L HIS
61L GLN
88L TRP
90L ASN
91L LYS
233 I1206
14E ASN
33D GLY
51E GLU
55E SER
56E GLN
57E HIS
58E ILE
61E GLN
88E TRP
90E ASN
91E LYS
SQ Y1205
53Q PRO
54Q GLY
55Q SER
56B GLN
57Q HIS
58Q ILE
59Q ASP
62Q LYS
SQ X1205
53E PRO
54E GLY
55E SER
56K GLN
57E HIS
58E ILE
59E ASP
62E LYS
SQ V2202
58D ILE
SQ W2202
58P ILE
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):

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.

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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
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
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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233 NAME: [5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLCARBAMOYL)-PENTYL]-CARBAMIC ACID METHYL ESTER
FORMULA: C14 H26 N2 O8
SMILES: COC(=O)NCCCCCC(=O)NC1OC(CO)C(O)C(O)C1O
SQ NAME: 3-ETHYLAMINO-4-METHYLAMINO-CYCLOBUTANE-1,2-DIONE
FORMULA: C7 H12 N2 O2
SMILES: CCNC1C(NC)C(=O)C1=O
CYN NAME: CYANIDE ION
FORMULA: C1 N1
SMILES: [C-]#N
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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