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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1rf6
TRANSFERASE HEADER
STRUCTURAL STUDIES OF STREPTOCOCCUS PNEUMONIAE EPSP SYNTHASE IN S3P-GLP BOUND STATE TITLE
5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE 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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GPJ A1428
20A LYS
24A HIS
47A ASP
90A ASN
91A SER
92A GLY
93A THR
120A ARG
168A GLN
312A ASP
339A LYS
340A GLU
343A ARG
384A HIS
385A ARG
S3P A1429
20A LYS
21A SER
25A ARG
93A THR
96A ARG
97A LEU
124A ARG
165A ALA
166A SER
167A ALA
168A GLN
193A ARG
311A ILE
312A ASP
335A GLU
338A VAL
339A LYS
GPJ C1628
20C LYS
24C HIS
47C ASP
90C ASN
91C SER
92C GLY
93C THR
120C ARG
168C GLN
312C ASP
339C LYS
340C GLU
343C ARG
384C HIS
385C ARG
S3P C1629
20C LYS
21C SER
25C ARG
93C THR
96C ARG
120C ARG
124C ARG
165C ALA
166C SER
167C ALA
168C GLN
193C ARG
262C ARG
311C ILE
312C ASP
335C GLU
339C LYS
GPJ D1728
20D LYS
47D ASP
90D ASN
91D SER
92D GLY
93D THR
120D ARG
168D GLN
312D ASP
339D LYS
340D GLU
343D ARG
384D HIS
385D ARG
S3P D1729
20D LYS
21D SER
25D ARG
93D THR
96D ARG
97D LEU
124D ARG
165D ALA
166D SER
167D ALA
168D GLN
193D ARG
311D ILE
312D ASP
335D GLU
339D LYS
GPJ B1528
20B LYS
24B HIS
47B ASP
90B ASN
91B SER
92B GLY
93B THR
120B ARG
168B GLN
312B ASP
339B LYS
340B GLU
343B ARG
384B HIS
385B ARG
S3P B1529
20B LYS
21B SER
25B ARG
93B THR
96B ARG
97B LEU
120B ARG
124B ARG
165B ALA
166B SER
167B ALA
168B GLN
193B ARG
311B ILE
312B ASP
335B GLU
339B 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
1rf5 Details
other holo-structures
pdb ID Ligand Unique ID
1rf4 SPQD1751 Details
SPQB1551
SPQC1651
SPQA1451
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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GPJ NAME: GLYPHOSATE
FORMULA: C3 H9 N1 O5 P1
SMILES: OC(=O)C[NH2+]CP(O)(O)=O
S3P NAME: SHIKIMATE-3-PHOSPHATE
FORMULA: C7 H11 O8 P1
SMILES: OC1CC(=CC(OP(O)(O)=O)C1O)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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