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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1f7r
VIRAL PROTEIN, HYDROLASE HEADER
CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS. TITLE
POL POLYPROTEIN 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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UDP F 138
19C ASP
52A ILE
55C LYS
56C SER
57C SER
65A VAL
66A LEU
67A GLY
68A GLY
69A VAL
70A ILE
71A ASP
74A TYR
77A GLU
78A ILE
79A GLY
81A ILE
100C GLN
122E ARG
126E GLY
127E TYR
128E GLY
129E SER
130E THR
UDP D 138
19A ASP
52E ILE
55A LYS
56A SER
57A SER
66E LEU
67E GLY
68E GLY
69E VAL
70E ILE
71E ASP
74E TYR
77E GLU
78E ILE
79E GLY
80E VAL
81E ILE
100A GLN
122C ARG
126C GLY
127C TYR
128C GLY
129C SER
130C THR
UDP B 138
19E ASP
52C ILE
55E LYS
56E SER
57E SER
66C LEU
67C GLY
68C GLY
69C VAL
70C ILE
71C ASP
74C TYR
77C GLU
78C ILE
79C GLY
80C VAL
81C ILE
100E GLN
122A ARG
126A GLY
127A TYR
128A GLY
129A SER
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1f7o Details
other holo-structures
pdb ID Ligand Unique ID
1f7q DUTE_801 Details
DUTC_802
1f7k UMPD_703 Details
UMPF_703
UMPB_703
1f7p UDPC_701 Details
UDPE_702
1f7n UMPF_337 Details
UMPD_337
UMPB_337
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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UDP NAME: URIDINE-5'-DIPHOSPHATE
FORMULA: C9 H14 N2 O12 P2
SMILES: OC1C(O)C(OC1COP(O)(=O)OP(O)(O)=O)N2C=CC(=O)NC2=O
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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