university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1tyu
VIRAL ADHESION PROTEIN HEADER
STRUCTURE OF TAILSPIKE-PROTEIN TITLE
TAILSPIKE PROTEIN 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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GLA E 5
236A VAL
237A SER
302A LYS
331A VAL
332A SER
335A GLN
359A GLU
363A LYS
365A TRP
TYV C 7
236A VAL
237A SER
240A VAL
391A TRP
TYV U 7
236S VAL
237S SER
240S VAL
391S TRP
GLA W 5
236S VAL
237S SER
302S LYS
331S VAL
332S SER
335S GLN
359S GLU
363S LYS
365S TRP
GLA N 5
236J VAL
237J SER
302J LYS
331J VAL
332J SER
335J GLN
359J GLU
363J LYS
365J TRP
TYV L 7
236J VAL
237J SER
240J VAL
391J TRP
RAM H 8
237A SER
359A GLU
360A SER
363A LYS
366A GLN
391A TRP
392A ASP
395A ASP
400A THR
RAM Z 8
237S SER
359S GLU
360S SER
363S LYS
366S GLN
391S TRP
392S ASP
395S ASP
400S THR
RAM Q 8
237J SER
359J GLU
360J SER
363J LYS
366J GLN
391J TRP
392J ASP
395J ASP
400J THR
MAN F 2
257A ASN
285A ARG
302A LYS
303A ASP
MAN X 2
257S ASN
285S ARG
302S LYS
303S ASP
MAN O 2
257J ASN
285J ARG
302J LYS
303J ASP
TYV Y 3
283S LEU
285S ARG
303S ASP
304S GLY
307S THR
309S GLU
335S GLN
337S LEU
365S TRP
TYV P 3
283J LEU
285J ARG
303J ASP
304J GLY
307J THR
309J GLU
335J GLN
337J LEU
365J TRP
GLA A 1
285S ARG
309S GLU
311S LEU
369S VAL
370S GLY
GLA R 1
285J ARG
309J GLU
311J LEU
369J VAL
370J GLY
MAN B 6
363A LYS
365A TRP
366A GLN
400A THR
MAN T 6
363S LYS
365S TRP
366S GLN
400S THR
MAN K 6
363J LYS
365J TRP
366J GLN
400J THR
RAM D 4
365A TRP
369A VAL
RAM V 4
365S TRP
369S VAL
RAM M 4
365J TRP
369J VAL
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
1tyv Details
other holo-structures
pdb ID Ligand Unique ID
1tyx ABEX___3 ABEY___7 RAMZ___4 MANW___6 MANV___2 GLAU___5 GLAT___1 Details
ABEF___3 MANE___6 ABEG___7 RAMI___8 MAND___2 GLAB___1 RAMH___4 GLAC___5
ABEO___3 MANN___6 RAMQ___4 GLAL___5 RAMR___8 GLAK___1 ABEP___7 MANM___2
1tyw GLAB___5 TYVH___7 GLAJ___1 RAME___8 MANC___2 MANF___6 GLCG___9 TYVD___3 RAMI___4 Details
GLAL___5 TYVN___3 MANP___6 RAMS___4 TYVR___7 RAMO___8 GLAT___1 GLCQ___9 MANM___2
GLAD___1 MANZ___6 RAMY___8 GLAV___5 TYVB___7 MANW___2 RAMC___4 TYVX___3 GLCA___9
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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GLA NAME: ALPHA D-GALACTOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
MAN NAME: ALPHA-D-MANNOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
RAM NAME: RHAMNOSE
FORMULA: C6 H12 O5
SMILES: CC1OC(O)C(O)C(O)C1O
TYV NAME: TYVELOSE
FORMULA: C6 H12 O4
SMILES: CC1OC(O)C(O)CC1O
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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