university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (redundant) - redundant
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apo-structureHelp

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

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2cbe
LYASE(OXO-ACID) HEADER
STRUCTURE OF NATIVE AND APO CARBONIC ANHYDRASE II AND SOME OF ITS ANION-LIGAND COMPLEXES TITLE
CARBONIC ANHYDRASE II 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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5 TRP
7 TYR
19 ASP
20 PHE
21 PRO
22 ILE
27 ARG
60 LEU
62 ASN
64 HIS
65 ALA
67 ASN
69 GLU
72 ASP
91 ILE
92 GLN
94 HIS
96 HIS
119 HIS
121 VAL
123 TRP
130 PHE
131 PHE
132 GLY
133 LYS
134 VAL
135 VAL
136 GLN
137 GLN
138 PRO
140 LEU
141 LEU
142 VAL
143 VAL
197 LEU
198 THR
199 THR
200 PRO
201 PRO
202 PRO
203 LEU
204 LEU
205 GLU
206 CYS
207 VAL
208 TRP
209 TRP
1005 TRP
1007 TYR
1057 LEU
1060 LEU
1062 ASN
1064 HIS
1065 ALA
1067 ASN
1069 GLU
1070 PHE
1071 ASP
1072 ASP
1073 SER
1091 ILE
1092 GLN
1094 HIS
1096 HIS
1119 HIS
1121 VAL
1131 PHE
1132 GLY
1135 VAL
1143 VAL
1198 LEU
1199 THR
1200 THR
1201 PRO
1202 PRO
1204 LEU
1207 VAL
1209 TRP
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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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-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
1okl MNS__862 _ZN__262 18 81 Details
1if9 SBBB_555 _ZNA_262 27 92 Details
1oq5 CELB_701 _ZNA_600 27 99 Details
1if8 SBSB_555 _ZNA_262 27 91 Details
2hl4 BO1B_264 _ZNA_262 GOLB_265 29 106 Details
1zge GOLB_900 SDAB_300 _ZNB1000 20 85 Details
1xq0 4TRB_270 _ZNA_262 28 103 Details
1cin MTS__262 _ZN__261 19 76 Details
1cil ETS__262 _ZN__261 20 83 Details
1i8z INLB_555 _ZNA_262 31 101 Details
1okn STB__555 _ZN__262 21 86 Details
2aw1 COXB_264 GOLB_266 _ZNB_262 29 117 Details
1ze8 GOLB_700 _ZNA_263 PIUA___1 28 103 Details
1z9y FUNB_500 _ZNB_300 22 92 Details
2qoa GOLA_802 _ZNA_262 MAJA_800 20 88 Details
2gd8 PO1B_264 PO1B_265 _ZNB_262 61 165 Details
1lug GOLB1003 _ZNA1001 SUAA1002 _HGA1005 25 101 Details
2hoc 1CNB_266 MBOA_267 32 80 Details
1CNB_265 _ZNB_263 GOLB_702 29 110
1zfq GOLB_900 _ZNB_600 ZECB_300 21 82 Details
1okm SAB__555 _ZN__262 19 71 Details
1cim PTS__262 _ZN__261 18 74 Details
1ttm 667B_264 _ZNB_262 22 81 Details
1if7 SBRB_555 _ZNA_262 27 88 Details
1i90 INMB_555 _ZNA_262 22 86 Details
2qp6 MB1A_800 _ZNA_262 15 75 Details
2qo8 3CCA_800 _ZNA_262 GOLA_802 30 97 Details
2hd6 BOSB_266 GOLB_264 _ZNB_262 27 102 Details
1i91 INQB_555 _ZNA_262 30 107 Details
1zgf TRUB_300 _ZNB_400 21 85 Details
2f14 FL1B1270 GOLB1266 _ZNB1262 GOLB1267 54 140 Details
1zfk GOLB1900 NR2B1400 _ZNB1300 31 110 Details
NR2B1500 24 70
v6.0
October 2008		 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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