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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1f74
LYASE HEADER
CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II COMPLEXED WITH 4-DEOXY-SIALIC ACID TITLE
N-ACETYL-NEURAMINATE 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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NAY K 951
10I ALA
43I TYR
46I GLY
47I SER
48I THR
136I TYR
164I LYS
166I THR
188I GLY
189I PHE
190I ASP
191I GLU
205I ILE
206I GLY
207I SER
208I THR
242I ILE
246I LEU
250I LEU
251I TYR
NAY P 951
10N ALA
43N TYR
46N GLY
47N SER
48N THR
136N TYR
164N LYS
166N THR
188N GLY
189N PHE
190N ASP
191N GLU
205N ILE
206N GLY
207N SER
208N THR
242N ILE
246N LEU
250N LEU
251N TYR
NAY B 950
10A ALA
43A TYR
46A GLY
47A SER
48A THR
136A TYR
164A LYS
166A THR
188A GLY
189A PHE
190A ASP
191A GLU
205A ILE
206A GLY
207A SER
208A THR
242A ILE
246A LEU
250A LEU
251A TYR
NAY F 950
10E ALA
43E TYR
46E GLY
47E SER
48E THR
136E TYR
164E LYS
166E THR
188E GLY
189E PHE
190E ASP
191E GLU
205E ILE
206E GLY
207E SER
208E THR
242E ILE
246E LEU
250E LEU
251E TYR
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
1f5z Details
other holo-structures
pdb ID Ligand Unique ID
1f7b NAVJ_902 Details
NAUB_901
NAVE_902
NAUG_901
1f73 HMNF_701 Details
HMNB_700
HMNI_703
HMND_702
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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NAY NAME: 6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-2-OXONONANOIC ACID
FORMULA: C11 H19 N1 O8
SMILES: CC(=O)NC(CCC(=O)C(O)=O)C(O)C(O)C(O)CO
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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