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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1mrl
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF STREPTOGRAMIN A ACETYLTRANSFERASE WITH DALFOPRISTIN TITLE
STREPTOGRAMIN A ACETYLTRANSFERASE 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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DOL F 301
11E ILE
14E ASN
16E SER
17E VAL
37E TYR
39E ASP
52C TYR
54C TYR
56C ILE
57C LEU
69E ILE
71E PRO
79C GLY
80C ALA
81C ASN
82C HIS
83C ARG
90C PRO
92C ASN
93C LEU
102C MET
103C PRO
108C LEU
DOL D 300
11C ILE
14C ASN
16C SER
17C VAL
37C TYR
39C ASP
52A TYR
54A TYR
56A ILE
57A LEU
79A GLY
80A ALA
81A ASN
82A HIS
83A ARG
90A PRO
92A ASN
93A LEU
102A MET
103A PRO
108A LEU
DOL B 302
11A ILE
14A ASN
16A SER
17A VAL
37A TYR
39A ASP
52E TYR
54E TYR
56E ILE
57E LEU
79E GLY
80E ALA
81E ASN
82E HIS
83E ARG
90E PRO
92E ASN
93E LEU
102E MET
103E PRO
105E LEU
108E LEU
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
1mr7 Details
other holo-structures
pdb ID Ligand Unique ID
3dho B2MC_304 Details
B2MC_303
B2MA_305
1mr9 ACOD_304 Details
ACOB_303
ACOF_305
1khr COAC_303 VIRB_402 Details
COAF_301 VIRE_401
COAH_302
1kk4 ACOF_301 Details
ACOB_303
ACOD_302
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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DOL NAME: 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE
FORMULA: C34 H50 N4 O9 S1
SMILES: CCN(CC)CCS(=O)(=O)C1CCN2C1C(=O)OC(C(C)C)C(C)C=CC(=O)NCC=CC(=CC(O)CC(=O)Cc3occ(n3)C2=O)C
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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