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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1f7k
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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UMP D 703
235E VAL
252E ILE
254C GLY
255C LYS
256C SER
257C SER
266E LEU
267E GLY
268E GLY
269E VAL
270E ILE
271E ASP
274E TYR
277E GLU
278E ILE
279E GLY
281E ILE
300C GLN
UMP F 703
235A VAL
252A ILE
254E GLY
255E LYS
256E SER
257E SER
266A LEU
267A GLY
268A GLY
269A VAL
270A ILE
271A ASP
274A TYR
277A GLU
278A ILE
279A GLY
280A VAL
281A ILE
300E GLN
UMP B 703
235C VAL
252C ILE
254A GLY
255A LYS
256A SER
257A SER
266C LEU
267C GLY
268C GLY
269C VAL
270C ILE
271C ASP
274C TYR
277C GLU
278C ILE
279C GLY
280C VAL
281C ILE
300A GLN
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
1f7o Details
other holo-structures
pdb ID Ligand Unique ID
1f7q DUTE_801 Details
DUTC_802
1f7r UDPF_138 Details
UDPD_138
UDPB_138
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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UMP NAME: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
FORMULA: C9 H13 N2 O8 P1
SMILES: OC1CC(OC1COP(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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