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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148l
HYDROLASE(O-GLYCOSYL) HEADER
A COVALENT ENZYME-SUBSTRATE INTERMEDIATE WITH SACCHARIDE DISTORTION IN A MUTANT T4 LYSOZYME TITLE
T4 LYSOZYME 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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AMU S 165
11E GLU
20E ASP
21E THR
22E GLU
24E TYR
26E GLU
30E GLY
32E LEU
35E LYS
104E PHE
105E GLN
141E GLN
142E THR
145E ARG
NAG S 164
30E GLY
31E HIS
32E LEU
35E LYS
70E ASP
103E VAL
104E PHE
105E GLN
106E MET
107E GLY
DAL S 166
35E LYS
105E GLN
106E MET
138E TRP
141E GLN
142E THR
DGL S 167
35E LYS
106E MET
110E GLY
114E PHE
136E SER
137E ARG
138E TRP
141E GLN
API S 169
110E GLY
113E GLY
114E PHE
115E THR
116E ASN
117E SER
132E ASN
135E LYS
136E SER
137E ARG
DAL S 170
137E ARG
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
180l 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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AMU NAME: N-ACETYLMURAMIC ACID
FORMULA: C11 H19 N1 O8
SMILES: CC(OC1C(O)C(CO)OC(O)C1NC(C)=O)C(O)=O
NAG NAME: N-ACETYL-D-GLUCOSAMINE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
DAL NAME: D-alanine
FORMULA: C3 H6 N1 O2
SMILES: CC(N)C(O)=OD-alanine
DGL NAME: D-GLUTAMIC ACID
FORMULA: C5 H9 N1 O4
SMILES: NC(CCC(O)=O)C(O)=O
API NAME: 2,6-DIAMINOPIMELIC ACID
FORMULA: C7 H14 N2 O4
SMILES: NC(CCCC(N)C(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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