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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3evl
LYASE HEADER
ALGINATE LYASE A1-III H192A COMPLEXED WITH TETRASACCHARIDE TITLE
ALGINATE LYASE 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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BEM A 403
67A ARG
68A TYR
80A TYR
88A ARG
138A GLN
141A TRP
245A HIS
246A TYR
249A TYR
306A ARG
314A ASP
342A ARG
BEM A 404
67A ARG
68A TYR
71A GLY
72A ASN
134A GLN
137A TYR
140A GLU
141A TRP
190A ASN
191A ASN
192A ALA
239A ARG
246A TYR
LGU A 402
67A ARG
88A ARG
249A TYR
306A ARG
312A ARG
314A ASP
340A ASP
342A ARG
BEM B 413
67B ARG
68B TYR
80B TYR
88B ARG
141B TRP
245B HIS
246B TYR
249B TYR
306B ARG
314B ASP
342B ARG
LGU B 412
67B ARG
88B ARG
249B TYR
306B ARG
312B ARG
314B ASP
340B ASP
342B ARG
BEM B 414
67B ARG
68B TYR
71B GLY
72B ASN
134B GLN
137B TYR
140B GLU
141B TRP
190B ASN
191B ASN
192B ALA
195B TRP
239B ARG
246B TYR
249B TYR
MAW A 401
88A ARG
311A GLY
312A ARG
313A GLY
314A ASP
332B GLY
339A PHE
MAW B 411
88B ARG
311B GLY
312B ARG
313B GLY
314B ASP
339B PHE
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
3evh 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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BEM NAME: not_found
FORMULA: not_found
SMILES: not_found
LGU NAME: L-GLUCURONIC ACID
FORMULA: C6 H10 O7
SMILES: OC1OC(C(O)C(O)C1O)C(O)=O
MAW NAME: 4-DEOXY-D-MANNURONIC ACID
FORMULA: C6 H8 O6
SMILES: OC1OC(=CC(O)C1O)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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