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LigASite database of binding sites |
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PDB ID and HEADER , TITLE and
COMPND records of the PDB file. | (click anywhere in this window to remove it) |
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1cwh |
COMPLEX (ISOMERASE/IMMUNOSUPPRESSANT) |
HEADER |
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HUMAN CYCLOPHILIN A COMPLEXED WITH 3-D-SER CYCLOSPORIN |
TITLE |
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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. | (click anywhere in this window to remove it) |
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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. | (click anywhere in this window to remove it) |
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BMT B 1 |
55 | A |
ARG |
63 | A |
GLN |
102 | A |
ASN |
103 | A |
ALA |
104 | A |
GLY |
126 | A |
HIS |
DSE B 3 |
71 | A |
ASN |
72 | A |
GLY |
73 | A |
THR |
ABA B 2 |
72 | A |
GLY |
73 | A |
THR |
101 | A |
ALA |
102 | A |
ASN |
103 | A |
ALA |
107 | A |
THR |
111 | A |
GLN |
MLE B 4 |
103 | A |
ALA |
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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. | (click anywhere in this window to remove it) |
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Links to external databases: LigPlot (hosted at the EBI):
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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. | (click anywhere in this window to remove it) |
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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. | (click anywhere in this window to remove it) |
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pdb ID |
1w8v |
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Details |
pdb ID |
Ligand Unique ID |
2rmb |
ABAF___2 DMTP___1 MLEF___4 DMTF___1 MLEP___4 ABAP___2 SARF___3 SARP___3 |
Details |
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ABAJ___2 MLEJ___4 ABAR___2 SARJ___3 SARR___3 MLER___4 DMTJ___1 DMTR___1 |
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ABAD___2 MLET___4 SART___3 DMTT___1 MLED___4 DMTD___1 SARD___3 ABAT___2 |
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ABAB___2 MLEL___4 SARL___3 SARB___3 DMTL___1 ABAL___2 DMTB___1 MLEB___4 |
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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 |
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ABAH___2 BMTR___1 MLEH___4 ABAR___2 SARR___3 MLER___4 BMTH___1 SARH___3 |
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ABAJ___2 MLEJ___4 MLET___4 BMTT___1 SART___3 SARJ___3 ABAT___2 BMTJ___1 |
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ABAB___2 MLEL___4 SARL___3 BMTB___1 SARB___3 ABAL___2 BMTL___1 MLEB___4 |
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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 |
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 |
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 |
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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 . | (click anywhere in this window to remove it) |
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ABA |
NAME: |
alpha-aminobutyric acid |
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FORMULA: |
C4 H8 N1 O2 |
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SMILES: |
CCC(N)C(O)=OALPHA-AMINOBUTYRIC ACID |
DSE |
NAME: |
N-METHYL-D-SERINE |
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FORMULA: |
C4 H9 N1 O3 |
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SMILES: |
CNC(CO)C(O)=O |
MLE |
NAME: |
N-methylleucine |
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FORMULA: |
C7 H14 N1 O2 |
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SMILES: |
CNC(CC(C)C)C(O)=ON-METHYLLEUCINE |
BMT |
NAME: |
4-methyl-4-[(E)-2-butenyl]-4,N-methyl-threonine |
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FORMULA: |
C10 H18 N1 O3 |
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SMILES: |
CNC(C(O)C(C)CC=CC)C(O)=O4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE |
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v9.2 January 2011 |
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 |
Script execution time: 1.3236 seconds |