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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1ixn
BIOSYNTHETIC PROTEIN HEADER
ENZYME-SUBSTRATE COMPLEX OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE 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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G3P J1003
9F ASN
12F HIS
20B ARG
43F THR
72F GLU
92F CYS
153F GLU
192F GLY
193F HIS
194F GLY
195F LEU
213F ASN
214F ILE
215F GLY
216F HIS
217F ALA
G3P I1003
9C ASN
12C HIS
20G ARG
43C THR
72C GLU
92C CYS
153C GLU
192C GLY
193C HIS
194C GLY
195C LEU
213C ASN
214C ILE
215C GLY
216C HIS
217C ALA
DXP I2001
9A ASN
11A ASP
12A HIS
20E ARG
45A HIS
47A ARG
51A ARG
52A HIS
72A GLU
94A VAL
101A VAL
102A THR
103A THR
133A PHE
193A HIS
G3P I1001
9A ASN
12A HIS
20E ARG
43A THR
72A GLU
153A GLU
193A HIS
194A GLY
195A LEU
213A ASN
214A ILE
215A GLY
216A HIS
217A ALA
DXP J2001
9E ASN
11E ASP
12E HIS
20A ARG
45E HIS
47E ARG
51E ARG
52E HIS
72E GLU
94E VAL
101E VAL
102E THR
103E THR
133E PHE
193E HIS
G3P J1001
9E ASN
12E HIS
20A ARG
43E THR
72E GLU
153E GLU
193E HIS
194E GLY
195E LEU
213E ASN
214E ILE
215E GLY
216E HIS
217E ALA
DXP I2003
9C ASN
11C ASP
12C HIS
20G ARG
45C HIS
47C ARG
51C ARG
52C HIS
72C GLU
94C VAL
101C VAL
102C THR
103C THR
133C PHE
193C HIS
DXP I2002
9B ASN
11B ASP
12B HIS
20F ARG
45B HIS
47B ARG
51B ARG
52B HIS
72B GLU
94B VAL
101B VAL
102B THR
103B THR
133B PHE
153B GLU
193B HIS
G3P I1002
9B ASN
12B HIS
20F ARG
43B THR
72B GLU
153B GLU
193B HIS
194B GLY
195B LEU
213B ASN
214B ILE
215B GLY
216B HIS
217B ALA
DXP I2004
9D ASN
11D ASP
12D HIS
20H ARG
45D HIS
47D ARG
51D ARG
52D HIS
72D GLU
94D VAL
101D VAL
102D THR
103D THR
133D PHE
193D HIS
G3P I1004
9D ASN
12D HIS
20H ARG
43D THR
72D GLU
133D PHE
153D GLU
193D HIS
194D GLY
195D LEU
213D ASN
214D ILE
215D GLY
216D HIS
217D ALA
DXP J2003
9F ASN
11F ASP
12F HIS
20B ARG
45F HIS
47F ARG
51F ARG
52F HIS
72F GLU
94F VAL
101F VAL
102F THR
103F THR
133F PHE
193F HIS
DXP J2002
9G ASN
11G ASP
12G HIS
20C ARG
45G HIS
47G ARG
51G ARG
52G HIS
72G GLU
94G VAL
101G VAL
102G THR
103G THR
133G PHE
153G GLU
193G HIS
G3P J1002
9G ASN
12G HIS
20C ARG
43G THR
72G GLU
153G GLU
193G HIS
194G GLY
195G LEU
213G ASN
214G ILE
215G GLY
216G HIS
217G ALA
DXP J2004
9H ASN
11H ASP
12H HIS
20D ARG
45H HIS
47H ARG
51H ARG
52H HIS
72H GLU
94H VAL
101H VAL
102H THR
103H THR
133H PHE
193H HIS
G3P J1004
9H ASN
12H HIS
20D ARG
43H THR
72H GLU
133H PHE
153H GLU
193H HIS
194H GLY
195H LEU
213H ASN
214H ILE
215H GLY
216H HIS
217H 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):

» Jmol
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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
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
1ho1 Details
other holo-structures
pdb ID Ligand Unique ID
1ixo G3PJ1003 G3PJ1005 Details
G3PI1003 G3PI1005
1ho4 PXPI_801 Details
PO4I_903 PXPI_804
PXPJ_801
PO4J_901 PXPJ_802
PO4J_903 PXPJ_804
PO4I_902 PXPI_803
PO4J_902 PXPJ_803
PO4I_901 PXPI_802
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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DXP NAME: 1-DEOXY-D-XYLULOSE-5-PHOSPHATE
FORMULA: C5 H11 O7 P1
SMILES: CC(=O)C(O)C(O)COP(O)(O)=O
G3P NAME: 3-PHOSPHOGLYCEROL
FORMULA: C3 H9 O6 P1
SMILES: OCC(O)COP(O)(O)=O
v6.0
October 2008
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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