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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2whh
HYDROLASE HEADER
HIV-1 PROTEASE TETHERED DIMER Q-PRODUCT COMPLEX ALONG WITH NUCLEOPHILIC WATER MOLECULE TITLE
POL PROTEIN 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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PPN A2201
8A ARG
23A LEU
25A ASP
28A ALA
50A ILE
80A THR
81A PRO
82A VAL
84A ILE
1025A ASP
1027A GLY
1028A ALA
1029A ASP
1048A GLY
1049A GLY
1050A ILE
GLU A2302
25A ASP
27A GLY
28A ALA
29A ASP
30A ASP
32A VAL
47A ILE
48A GLY
84A ILE
1008A ARG
1050A ILE
PPN A2301
25A ASP
27A GLY
28A ALA
48A GLY
49A GLY
50A ILE
1008A ARG
1023A LEU
1025A ASP
1050A ILE
1081A PRO
1082A VAL
1084A ILE
GLU A2202
50A ILE
1025A ASP
1027A GLY
1028A ALA
1029A ASP
1030A ASP
1032A VAL
1047A ILE
1048A GLY
1084A ILE
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
1lv1 Details
other holo-structures
pdb ID Ligand Unique ID
none
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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GLU NAME: L-Glutamic acid
FORMULA: C5 H8 N1 O4
SMILES: NC(CCC(O)=O)C(O)=OGLUTAMIC ACID
PPN NAME: PARA-NITROPHENYLALANINE
FORMULA: C9 H10 N2 O4
SMILES: NC(Cc1ccc(cc1)[N+]([O-])=O)C(O)=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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