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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3hiv
HYDROLASE/HYDROLASE INHIBITOR HEADER
CRYSTAL STRUCTURE OF SAPORIN-L1 IN COMPLEX WITH THE TRINUCLEOTIDE INHIBITOR, A TRANSITION STATE ANALOGUE TITLE
VACUOLAR SAPORIN 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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TXN B 260
68B GLN
70B SER
71B ASN
72B LEU
73B TYR
74B VAL
91B PHE
94B PHE
95B GLN
121B GLU
122B SER
123B TYR
124B PRO
126B ILE
169B VAL
174B GLU
177B ARG
206B GLU
207B ASN
208B ASN
209B TRP
210B GLY
211B LEU
214B ARG
233B TYR
254B LEU
256B VAL
TXN A 260
68A GLN
70A SER
71A ASN
72A LEU
73A TYR
74A VAL
91A PHE
94A PHE
95A GLN
121A GLU
122A SER
123A TYR
124A PRO
126A ILE
169A VAL
173A GLY
174A GLU
177A ARG
206A GLU
207A ASN
208A ASN
209A TRP
210A GLY
211A LEU
214A ARG
233A TYR
254A LEU
256A VAL
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
3his Details
other holo-structures
pdb ID Ligand Unique ID
3hit DYNA_260 Details
DYNB_260
3hiw C2XA_260 C2XB_260 Details
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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TXN NAME: not_found
FORMULA: not_found
SMILES: not_found
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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