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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1ho4
BIOSYNTHETIC PROTEIN HEADER
CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX WITH PYRIDOXINE 5'-PHOSPHATE AND INORGANIC PHOSPHATE TITLE
PYRIDOXINE 5'-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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PO4 B 901
9A ASN
11A ASP
12A HIS
20D ARG
45A HIS
47A ARG
51A ARG
52A HIS
101A VAL
102A THR
103A THR
PXP C 802
9A ASN
12A HIS
20D ARG
45A HIS
72A GLU
92A CYS
94A VAL
102A THR
103A THR
133A PHE
153A GLU
192A GLY
193A HIS
194A GLY
195A LEU
213A ASN
214A ILE
215A GLY
216A HIS
217A ALA
PO4 E 901
9D ASN
11D ASP
12D HIS
20A ARG
45D HIS
47D ARG
51D ARG
52D HIS
101D VAL
102D THR
103D THR
PXP F 802
9D ASN
12D HIS
20A ARG
45D HIS
72D GLU
92D CYS
94D VAL
102D THR
103D THR
133D PHE
153D GLU
192D GLY
193D HIS
194D GLY
195D LEU
213D ASN
214D ILE
215D GLY
216D HIS
217D ALA
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
1ho1 Details
other holo-structures
pdb ID Ligand Unique ID
1ixo G3PC1003 G3PE1005 Details
1ixn DXPB2002 G3PC1002 Details
DXPE2003 G3PF1003
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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PO4 NAME: PHOSPHATE ION
FORMULA: O4 P1
SMILES: [O-]P([O-])([O-])=O
PXP NAME: PYRIDOXINE-5'-PHOSPHATE
FORMULA: C8 H12 N1 O6 P1
SMILES: Cc1ncc(COP(O)(O)=O)c(CO)c1O
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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