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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1tjw
LYASE HEADER
CRYSTAL STRUCTURE OF T161D DUCK DELTA 2 CRYSTALLIN MUTANT WITH BOUND ARGININOSUCCINATE TITLE
DELTA CRYSTALLIN II 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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AS1 B1001
29C SER
33C ASP
89C ASP
91C HIS
110C HIS
114C SER
115C ARG
116C ASN
119C VAL
161A ASP
162A HIS
205C ALA
238C ARG
281E THR
291E ASN
293E ASP
323C TYR
325C LYS
327C LEU
328C GLN
331C LYS
AS1 H1003
29E SER
33E ASP
88E GLU
89E ASP
91E HIS
110E HIS
114E SER
115E ARG
116E ASN
119E VAL
161G ASP
162G HIS
205E ALA
238E ARG
281C THR
291C ASN
293C ASP
323E TYR
325E LYS
327E LEU
328E GLN
331E LYS
AS1 D1004
29A SER
33A ASP
89A ASP
91A HIS
110A HIS
114A SER
115A ARG
116A ASN
119A VAL
161C ASP
162C HIS
205A ALA
238A ARG
281G THR
289G LYS
291G ASN
293G ASP
323A TYR
325A LYS
327A LEU
328A GLN
331A LYS
AS1 F1002
29G SER
33G ASP
89G ASP
91G HIS
110G HIS
114G SER
115G ARG
116G ASN
119G VAL
161E ASP
162E HIS
205G ALA
238G ARG
281A THR
291A ASN
293A ASP
323G TYR
325G LYS
327G LEU
328G GLN
331G LYS
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
1tjv 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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AS1 NAME: ARGININOSUCCINATE
FORMULA: C10 H18 N4 O6
SMILES: NC(CCCNC(=N)NC(CC(O)=O)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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