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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1kgz
TRANSFERASE HEADER
CRYSTAL STRUCTURE ANALYSIS OF THE ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE FROM ERWINIA CAROTOVORA (CURRENT NAME, PECTOBACTERIUM CAROTOVORUM) TITLE
ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE 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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PRP H 700
90F VAL
91F GLY
92F THR
93F GLY
94F GLY
95F ASP
100F ILE
101F ASN
102F ILE
103F SER
104F THR
119F LYS
121F GLY
122F ASN
124F SER
130F ALA
131F GLY
132F SER
237F GLU
PRP C 600
90A VAL
91A GLY
92A THR
93A GLY
94A GLY
95A ASP
96A GLY
100A ILE
101A ASN
102A ILE
103A SER
104A THR
119A LYS
121A GLY
122A ASN
124A SER
131A GLY
132A SER
237A GLU
MN J 500
91F GLY
103F SER
236F ASP
237F GLU
MN E 500
91A GLY
103A SER
236A ASP
237A GLU
MN I 501
93F GLY
95F ASP
99F SER
100F ILE
236F ASP
237F GLU
MN D 501
93A GLY
95A ASP
99A SER
100A ILE
235A MET
236A ASP
237A GLU
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
1khd 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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PRP NAME: ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
FORMULA: C5 H13 O14 P3
SMILES: OC1C(O)C(OC1COP(O)(O)=O)OP(O)(=O)OP(O)(O)=O
MN NAME: MANGANESE (II) ION
FORMULA: MN1
SMILES: [Mn++]
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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