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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PXP I 801
9D ASN
11D ASP
12D HIS
20H ARG
45D HIS
72D GLU
92D CYS
94D VAL
133D PHE
153D GLU
192D GLY
193D HIS
194D GLY
195D LEU
213D ASN
214D ILE
215D GLY
216D HIS
217D ALA
PO4 I 903
9B ASN
11B ASP
12B HIS
20G ARG
45B HIS
47B ARG
51B ARG
52B HIS
101B VAL
102B THR
103B THR
PXP I 804
9B ASN
12B HIS
20G ARG
24G TYR
45B HIS
72B GLU
92B CYS
94B VAL
103B THR
133B PHE
153B GLU
192B GLY
193B HIS
194B GLY
195B LEU
213B ASN
214B ILE
215B GLY
216B HIS
217B ALA
PXP J 801
9H ASN
11H ASP
12H HIS
20D ARG
45H HIS
72H GLU
92H CYS
94H VAL
133H PHE
153H GLU
192H GLY
193H HIS
194H GLY
195H LEU
213H ASN
214H ILE
215H GLY
216H HIS
217H ALA
PO4 J 901
9E ASN
11E ASP
12E HIS
20A ARG
45E HIS
47E ARG
51E ARG
52E HIS
101E VAL
102E THR
103E THR
PXP J 802
9E ASN
12E HIS
20A ARG
45E HIS
72E GLU
92E CYS
94E VAL
102E THR
103E THR
133E PHE
153E GLU
192E GLY
193E HIS
194E GLY
195E LEU
213E ASN
214E ILE
215E GLY
216E HIS
217E ALA
PO4 J 903
9F ASN
11F ASP
12F HIS
20C ARG
45F HIS
47F ARG
51F ARG
52F HIS
101F VAL
102F THR
103F THR
PXP J 804
9F ASN
12F HIS
20C ARG
24C TYR
45F HIS
72F GLU
92F CYS
94F VAL
103F THR
133F PHE
153F GLU
192F GLY
193F HIS
194F GLY
195F LEU
213F ASN
214F ILE
215F GLY
216F HIS
217F ALA
PO4 I 902
9C ASN
11C ASP
12C HIS
20F ARG
45C HIS
47C ARG
51C ARG
52C HIS
101C VAL
102C THR
103C THR
PXP I 803
9C ASN
12C HIS
20F ARG
45C HIS
72C GLU
92C CYS
94C VAL
102C THR
103C THR
133C PHE
153C GLU
193C HIS
194C GLY
195C LEU
213C ASN
214C ILE
215C GLY
216C HIS
217C ALA
PO4 J 902
9G ASN
11G ASP
12G HIS
20B ARG
45G HIS
47G ARG
51G ARG
52G HIS
101G VAL
102G THR
103G THR
PXP J 803
9G ASN
12G HIS
20B ARG
45G HIS
72G GLU
92G CYS
94G VAL
102G THR
103G THR
133G PHE
153G GLU
193G HIS
194G GLY
195G LEU
213G ASN
214G ILE
215G GLY
216G HIS
217G ALA
PO4 I 901
9A ASN
11A ASP
12A HIS
20E ARG
45A HIS
47A ARG
51A ARG
52A HIS
101A VAL
102A THR
103A THR
PXP I 802
9A ASN
12A HIS
20E 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
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):

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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
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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 G3PJ1003 G3PJ1005 Details
G3PI1003 G3PI1005
1ixn DXPI2001 G3PI1001 Details
DXPJ2001 G3PJ1001
DXPI2003 G3PI1003
DXPI2002 G3PI1002
DXPI2004 G3PI1004
DXPJ2003 G3PJ1003
DXPJ2002 G3PJ1002
DXPJ2004 G3PJ1004
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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PXP NAME: PYRIDOXINE-5'-PHOSPHATE
FORMULA: C8 H12 N1 O6 P1
SMILES: Cc1ncc(COP(O)(O)=O)c(CO)c1O
PO4 NAME: PHOSPHATE ION
FORMULA: O4 P1
SMILES: [O-]P([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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