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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1w8v
ISOMERASE HEADER
ENZYMATIC AND STRUCTURAL CHARACTERIZATION OF NON PEPTIDE LIGAND CYCLOPHILIN COMPLEXES TITLE
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A 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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54 HIS
55 ARG
57 ILE
58 PRO
59 GLY
60 PHE
61 MET
63 GLN
67 PHE
69 ARG
71 ASN
72 GLY
73 THR
74 GLY
75 GLY
81 GLU
82 LYS
101 ALA
102 ASN
103 ALA
104 GLY
107 THR
109 GLY
110 SER
111 GLN
113 PHE
117 ALA
118 LYS
119 THR
121 TRP
122 LEU
125 LYS
126 HIS
148 ARG
149 ASN
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
2rmb ABAF___2 DMTP___1 MLEF___4 DMTF___1 MLEP___4 ABAP___2 SARF___3 SARP___3 68 196 Details
ABAJ___2 MLEJ___4 ABAR___2 SARJ___3 SARR___3 MLER___4 DMTJ___1 DMTR___1 68 200
ABAD___2 MLET___4 SART___3 DMTT___1 MLED___4 DMTD___1 SARD___3 ABAT___2 68 197
ABAB___2 MLEL___4 SARL___3 SARB___3 DMTL___1 ABAL___2 DMTB___1 MLEB___4 68 199
ABAH___2 MLEH___4 MLEN___4 DMTN___1 ABAN___2 SARN___3 DMTH___1 SARH___3 68 194
1cwb ABAB___2 DMTB___1 MLEB___4 SARB___3 34 81 Details
3odl ABAB___6 MVAB___4 SARB___7 YYAB___5 MLEB___2 DALB___1 MLEB___3 MLEB___8 65 150 Details
2rma ABAF___2 BMTP___1 MLEF___4 MLEP___4 ABAP___2 BMTF___1 SARF___3 SARP___3 66 197 Details
ABAH___2 BMTR___1 MLEH___4 ABAR___2 SARR___3 MLER___4 BMTH___1 SARH___3 66 199
ABAJ___2 MLEJ___4 MLET___4 BMTT___1 SART___3 SARJ___3 ABAT___2 BMTJ___1 66 189
ABAB___2 MLEL___4 SARL___3 BMTB___1 SARB___3 ABAL___2 BMTL___1 MLEB___4 66 190
ABAD___2 BMTD___1 MLEN___4 MLED___4 BMTN___1 ABAN___2 SARD___3 SARN___3 66 196
3cys ABAB_202 SARB_203 BMTB_201 MLEB_204 33 82 Details
1cwl ABAB___2 MHLB___4 SARB___3 BMTB___1 34 80 Details
1cwh ABAB___2 DSEB___3 MLEB___4 BMTB___1 35 78 Details
1cwc BMTB___1 DBBB___2 SARB___3 MNLB___4 34 76 Details
1ynd SFAB_401 SFAD_402 156 348 Details
1mf8 ABAG___2 BMTG___1 MLEG___4 SARG___3 33 126 Details
1mik AA4B___2 MLEB___4 SARB___3 BMTB___1 35 94 Details
3odi ABAB___6 MVAB___4 SARB___7 MLEB___2 DALB___1 MLEB___3 XXAB___5 MLEB___8 65 158 Details
1nmk SFMA_166 SFMB_201 106 286 Details
1cwm ABAB___2 TBMB___1 IMLB___4 SARB___3 33 74 Details
1cwa ABAB___2 MLEB___4 SARB___3 BMTB___1 33 75 Details
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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