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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1w6h
HYDROLASE HEADER
NOVEL PLASMEPSIN II-INHIBITOR COMPLEX TITLE
PLASMEPSIN 2 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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TIT B1330
15A MET
32A ILE
34A ASP
36A GLY
37A SER
38A ALA
75A MET
76A ASN
77A TYR
78A VAL
79A SER
111A PHE
114A THR
115A TYR
120A PHE
123A ILE
131A LEU
133A ILE
192A TYR
214A ASP
216A GLY
217A THR
218A SER
219A ALA
221A THR
290A ILE
292A LEU
294A PHE
300A ILE
TIT D1330
15C MET
32C ILE
34C ASP
36C GLY
37C SER
38C ALA
75C MET
76C ASN
77C TYR
78C VAL
79C SER
111C PHE
114C THR
120C PHE
123C ILE
131C LEU
133C ILE
192C TYR
214C ASP
216C GLY
217C THR
218C SER
219C ALA
221C THR
290C ILE
292C LEU
294C PHE
300C 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
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
1lf4 Details
other holo-structures
pdb ID Ligand Unique ID
1xdh IHND1348 Details
IHNB1347
1w6i IHNB1330 Details
IHND1330
1lf3 EH5B_332 Details
EH5D_332
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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TIT NAME: N-((3S,4S)-5-[(4-bromobenzyl)oxy]-3-hydroxy-4-{[N-(pyridin-2-ylcarbonyl)-L-valyl]amino}pentanoyl)-L-alanyl-L-leucinamide
FORMULA: C32 H45 N6 O7 BR1
SMILES: CC(C)CC(NC(=O)C(C)NC(=O)CC(O)C(COCc1ccc(Br)cc1)NC(=O)C(NC(=O)c2ccccn2)C(C)C)C(N)=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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