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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1f7b
LYASE HEADER
CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-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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NAV J 902
10H ALA
43H TYR
46H GLY
47H SER
48H THR
136H TYR
164H LYS
166H THR
188H GLY
189H PHE
190H ASP
191H GLU
205H ILE
206H GLY
207H SER
208H THR
242H ILE
246H LEU
250H LEU
251H TYR
NAU B 901
10A ALA
43A TYR
46A GLY
47A SER
48A THR
136A TYR
138A ILE
140A PHE
141A LEU
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
NAV E 902
10C ALA
43C TYR
46C GLY
47C SER
48C THR
136C TYR
164C LYS
166C THR
188C GLY
189C PHE
190C ASP
191C GLU
205C ILE
206C GLY
207C SER
208C THR
242C ILE
246C LEU
250C LEU
251C TYR
NAU G 901
10F ALA
43F TYR
46F GLY
47F SER
48F THR
136F TYR
138F ILE
140F PHE
141F LEU
164F LYS
166F THR
188F GLY
189F PHE
190F ASP
191F GLU
205F ILE
206F GLY
207F SER
208F THR
242F ILE
246F LEU
250F LEU
251F 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
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).

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apo-structure
pdb ID
1f6p Details
other holo-structures
pdb ID Ligand Unique ID
1f74 NAYK_951 Details
NAYP_951
NAYB_950
NAYF_950
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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NAV NAME: 6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC ACID
FORMULA: C11 H19 N1 O8
SMILES: CC(=O)NC(C(O)C(O)C(O)CO)C(=O)CCC(O)=O
NAU NAME: 4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC ACID
FORMULA: C11 H21 N1 O9
SMILES: CC(=O)NC(C(O)C(O)C(O)CO)C(O)(O)CCC(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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