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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1s3f
TRANSFERASE HEADER
PURINE 2'-DEOXYRIBOSYLTRANSFERASE + SELENOINOSINE TITLE
PURINE TRANS DEOXYRIBOSYLASE 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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SNI D 747
11C TYR
13C GLY
14C SER
15C PRO
44C PRO
45C PHE
59C ILE
67C TRP
71C THR
75C ASP
79C ILE
95C ASP
97C GLY
98C SER
101C GLU
128A ASN
129A LEU
130A MET
166A ILE
167A TYR
SNI L 747
11K TYR
13K GLY
14K SER
15K PRO
44K PRO
45K PHE
59K ILE
67K TRP
71K THR
75K ASP
79K ILE
95K ASP
97K GLY
98K SER
101K GLU
128I ASN
129I LEU
130I MET
166I ILE
167I TYR
SNI B 745
11A TYR
13A GLY
14A SER
15A PRO
44A PRO
45A PHE
59A ILE
67A TRP
71A THR
75A ASP
95A ASP
97A GLY
98A SER
101A GLU
128C ASN
129C LEU
130C MET
167C TYR
SNI J 745
11I TYR
13I GLY
14I SER
15I PRO
44I PRO
45I PHE
59I ILE
67I TRP
71I THR
75I ASP
95I ASP
97I GLY
98I SER
101I GLU
128K ASN
129K LEU
130K MET
167K TYR
SNI F 746
11E TYR
13E GLY
14E SER
15E PRO
17E TYR
44E PRO
45E PHE
59E ILE
67E TRP
71E THR
75E ASP
95E ASP
97E GLY
98E SER
101E GLU
128G ASN
129G LEU
130G MET
166G ILE
167G TYR
SNI H 746
11G TYR
13G GLY
14G SER
15G PRO
17G TYR
44G PRO
45G PHE
59G ILE
67G TRP
71G THR
75G ASP
95G ASP
97G GLY
98G SER
101G GLU
128E ASN
129E LEU
130E MET
166E ILE
167E TYR
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
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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).

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apo-structure
pdb ID
1s2l Details
other holo-structures
pdb ID Ligand Unique ID
1s2g 3D1D1168 Details
3D1H1169
3D1B1170
3D1J1170
3D1F1169
3D1L1168
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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SNI NAME: 9-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YL)-1,9-DIHYDRO-PURINE-6-THIONE
FORMULA: C10 H12 N4 O4 SE1
SMILES: OCC1OC(C(O)C1O)[n]2cnc3C(=[Se])NC=Nc23
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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