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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2web
HYDROLASE HEADER
ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL(2S)-[1-(((N-FORMYL)-L- VALYL)AMINO-2-(2-NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3- PHENYLPROPANOATE, SODIUM SALT TITLE
PENICILLOPEPSIN 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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PP4 H 326
16F GLU
31F ASN
33F ASP
35F GLY
36F SER
68A GLY
73F ILE
74F SER
75F TYR
76F GLY
77F ASP
79F SER
111F GLN
112F PHE
115F ASP
118F ASN
121F LEU
129F ILE
133A GLN
134A PRO
190F PHE
211F ILE
213F ASP
215F GLY
216F THR
217F THR
218F LEU
220F LEU
293F ILE
295F PHE
297F ILE
PP4 C 326
16A GLU
31A ASN
33A ASP
35A GLY
36A SER
68F GLY
73A ILE
74A SER
75A TYR
76A GLY
77A ASP
79A SER
111A GLN
112A PHE
115A ASP
118A ASN
121A LEU
129A ILE
133F GLN
134F PRO
190A PHE
211A ILE
213A ASP
215A GLY
216A THR
217A THR
218A LEU
220A LEU
293A ILE
295A PHE
297A 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
3app Details
other holo-structures
pdb ID Ligand Unique ID
2wea PP6C_326 Details
PP6H_326
2wed PP6A_327 Details
1bxo PP7A_324 Details
1bxq ACTA_330 PP8A_324 Details
2wec PP5H_326 Details
PP5C_326
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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PP4 NAME: METHYL (2S)-[1-((N-FORMYL)-L-VALYL)AMINO-2-(2-NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYL PROPANOATE
FORMULA: C28 H32 N2 O7 P1
SMILES: COC(=O)C(Cc1ccccc1)OP([O-])(=O)C(Cc2ccc3ccccc3c2)NC(=O)C(NC=O)C(C)C
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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