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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1pw8
HYDROLASE HEADER
COVALENT ACYL ENZYME COMPLEX OF THE R61 DD-PEPTIDASE WITH A HIGHLY SPECIFIC CEPHALOSPORIN TITLE
D-ALANYL-D-ALANINE CARBOXYPEPTIDASE 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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H2A A 400
61A GLY
62A SER
65A LYS
114A ASP
116A THR
120A PHE
121A ALA
123A THR
159A TYR
161A ASN
214A LEU
217A ASP
233A TRP
237A ALA
238A GLY
285A ARG
299A THR
300A GLY
301A THR
303A GLN
326A SER
327A ASN
332A LEU
GOL A 500
301A THR
306A TYR
327A ASN
329A VAL
332A LEU
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).

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apo-structure
pdb ID
3pte Details
other holo-structures
pdb ID Ligand Unique ID
1pwd CSCA_400 Details
1ceg CEPA_400 Details
1pwg HELA_400 Details
1iki DALA_500 REYA_400 Details
1hvb CEHA_401 Details
1cef CEFA_400 Details
1ikg REXA_400 Details
1mpl GOLA_500 RE1A_400 GOLA_501 Details
1scw CP5A_400 GOLA_500 GOLA_504 Details
1pw1 FORA_600 HELA_400 FORA_601 Details
1pwc PNMA_400 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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GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
H2A NAME: (6R,7R)-3-[(ACETYLOXY)METHYL]-7-{[(6S)-6-(GLYCYLAMINO)-7-OXIDO-7-OXOHEPTANOYL]AMINO}-8-OXO-5-THIA-1-AZABICYCLO[4.2.0]OCTANE-2-CARBOXYLATE
FORMULA: C19 H27 N4 O9 S1
SMILES: CC(=O)OCC1CSC2C(NC(=O)CCCCC(NC(=O)C[NH3+])C([O-])=O)C(=O)N2C1C([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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