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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3odl
ISOMERASE/IMMUNOSUPPRESSANT HEADER
CRYSTAL STRUCTURE OF CYCLOPHILIN A IN COMPLEX WITH VOCLOSPOR ISA247 TITLE
CYCLOPHILIN A 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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SAR B 7
54A HIS
71A ASN
72A GLY
73A THR
YYA B 5
54A HIS
55A ARG
63A GLN
102A ASN
103A ALA
104A GLY
126A HIS
MVA B 4
55A ARG
60A PHE
61A MET
63A GLN
101A ALA
102A ASN
113A PHE
122A LEU
126A HIS
MLE B 3
55A ARG
60A PHE
121A TRP
122A LEU
126A HIS
MLE B 2
57A ILE
59A GLY
60A PHE
121A TRP
122A LEU
148A ARG
DAL B 1
57A ILE
ABA B 6
72A GLY
73A THR
101A ALA
102A ASN
103A ALA
107A THR
111A GLN
MLE B 8
103A ALA
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
1w8v Details
other holo-structures
pdb ID Ligand Unique ID
2rmb ABAF___2 DMTP___1 MLEF___4 DMTF___1 MLEP___4 ABAP___2 SARF___3 SARP___3 Details
ABAJ___2 MLEJ___4 ABAR___2 SARJ___3 SARR___3 MLER___4 DMTJ___1 DMTR___1
ABAD___2 MLET___4 SART___3 DMTT___1 MLED___4 DMTD___1 SARD___3 ABAT___2
ABAB___2 MLEL___4 SARL___3 SARB___3 DMTL___1 ABAL___2 DMTB___1 MLEB___4
ABAH___2 MLEH___4 MLEN___4 DMTN___1 ABAN___2 SARN___3 DMTH___1 SARH___3
1cwb ABAB___2 DMTB___1 MLEB___4 SARB___3 Details
2rma ABAF___2 BMTP___1 MLEF___4 MLEP___4 ABAP___2 BMTF___1 SARF___3 SARP___3 Details
ABAH___2 BMTR___1 MLEH___4 ABAR___2 SARR___3 MLER___4 BMTH___1 SARH___3
ABAJ___2 MLEJ___4 MLET___4 BMTT___1 SART___3 SARJ___3 ABAT___2 BMTJ___1
ABAB___2 MLEL___4 SARL___3 BMTB___1 SARB___3 ABAL___2 BMTL___1 MLEB___4
ABAD___2 BMTD___1 MLEN___4 MLED___4 BMTN___1 ABAN___2 SARD___3 SARN___3
3cys ABAB_202 SARB_203 BMTB_201 MLEB_204 Details
1cwl ABAB___2 MHLB___4 SARB___3 BMTB___1 Details
1cwh ABAB___2 DSEB___3 MLEB___4 BMTB___1 Details
1cwc BMTB___1 DBBB___2 SARB___3 MNLB___4 Details
1ynd SFAB_401 SFAD_402 Details
1mf8 ABAG___2 BMTG___1 MLEG___4 SARG___3 Details
1mik AA4B___2 MLEB___4 SARB___3 BMTB___1 Details
3odi ABAB___6 MVAB___4 SARB___7 MLEB___2 DALB___1 MLEB___3 XXAB___5 MLEB___8 Details
1nmk SFMA_166 SFMB_201 Details
1cwm ABAB___2 TBMB___1 IMLB___4 SARB___3 Details
1cwa ABAB___2 MLEB___4 SARB___3 BMTB___1 Details
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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ABA NAME: alpha-aminobutyric acid
FORMULA: C4 H8 N1 O2
SMILES: CCC(N)C(O)=OALPHA-AMINOBUTYRIC ACID
MVA NAME: N-methylvaline
FORMULA: C6 H12 N1 O2 Q3
SMILES: CNC(C(C)C)C(O)=ON-METHYLVALINE
SAR NAME: sarcosine
FORMULA: C3 H6 N1 O2
SMILES: CNCC(O)=OSARCOSINE
YYA NAME: not_found
FORMULA: not_found
SMILES: not_found
MLE NAME: N-methylleucine
FORMULA: C7 H14 N1 O2
SMILES: CNC(CC(C)C)C(O)=ON-METHYLLEUCINE
DAL NAME: D-alanine
FORMULA: C3 H6 N1 O2
SMILES: CC(N)C(O)=OD-alanine
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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