university lille north of france LigASite database of binding sites
apo-structureHelp

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

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2dhq
DEHYDRATASE HEADER
3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS TITLE
PROTEIN (3-DEHYDROQUINATE DEHYDRATASE) COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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11 PRO
12 ASN
13 LEU
15 ARG
16 LEU
17 GLY
18 ARG
19 ARG
20 GLU
24 TYR
25 GLY
63 HIS
75 ASN
77 GLY
78 GLY
81 HIS
84 VAL
87 ARG
88 ASP
89 ALA
91 ALA
92 GLU
101 HIS
102 ILE
103 SER
105 VAL
106 HIS
108 ARG
109 GLU
110 GLU
111 PHE
112 ARG
113 ARG
114 HIS
115 SER
116 TYR
118 SER
119 PRO
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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
2y77 CB8P1144 29 84 Details
CB8R1144 29 83
CB8B1144 29 83
CB8T1144 29 83
CB8V1144 29 80
CB8F1144 29 80
CB8N1144 29 80
CB8X1144 29 81
CB8L1144 29 83
CB8D1144 29 81
CB8H1144 29 83
CB8J1144 29 81
2xb8 SO4P1146 SO4S1148 SO4U1150 15 89 Details
SO4C1148 SO4E1150 SO4Z1146 15 87
XNWW1144 22 92
SO4A1150 SO4Y1148 SO4V1146 15 89
SO4B1146 SO4G1150 SO4E1148 15 90
XNWQ1144 22 92
SO4L1146 SO4Q1150 SO4O1148 15 86
SO4D1146 SO4G1148 SO4I1150 15 90
SO4J1146 SO4M1148 SO4O1150 15 86
SO4N1146 SO4Q1148 SO4S1150 15 89
XNWU1144 22 94
XNWG1144 22 91
SO4H1146 SO4M1150 SO4K1148 15 89
SO4A1148 SO4X1146 SO4C1150 15 90
XNWI1144 22 92
XNWM1144 22 94
SO4R1146 SO4W1150 SO4U1148 15 90
XNWA1144 22 96
XNWO1144 22 91
XNWC1144 22 96
SO4F1146 SO4K1150 SO4I1148 15 87
XNWK1144 22 92
XNWY1144 22 92
XNWE1144 22 92
1h0s FA6H_200 14 70 Details
FA6R_200 14 70
2y76 CB7J1144 33 119 Details
CB7R1144 33 120
CB7L1144 33 119
CB7F1144 33 115
CB7B1144 33 116
CB7X1144 33 115
CB7T1144 33 116
CB7D1144 33 118
CB7H1144 33 118
CB7N1144 33 121
CB7V1144 33 120
CB7P1144 33 121
2y71 CB6L1144 24 113 Details
CB6V1144 24 110
CB6D1144 24 113
CB6P1144 24 109
CB6B1144 24 110
CB6F1144 24 113
CB6T1144 24 108
CB6J1144 24 108
CB6N1144 24 108
CB6X1144 24 113
CB6R1144 24 108
CB6H1144 24 109
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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