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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1hmp
TRANSFERASE (GLYCOSYLTRANSFERASE) HEADER
THE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH BOUND GMP TITLE
HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE 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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5GP D 800
68C LYS
133C GLU
134C ASP
135C ILE
136C ILE
137C ASP
138C THR
139C GLY
140C LYS
141C THR
165C LYS
186C PHE
187C VAL
188C VAL
192C LEU
193C ASP
5GP B 300
68A LYS
133A GLU
134A ASP
135A ILE
136A ILE
137A ASP
138A THR
139A GLY
140A LYS
141A THR
142A MET
165A LYS
185A LYS
186A PHE
187A VAL
188A VAL
192A LEU
193A ASP
5GP H 800
68G LYS
133G GLU
134G ASP
135G ILE
136G ILE
137G ASP
138G THR
139G GLY
140G LYS
141G THR
165G LYS
186G PHE
187G VAL
188G VAL
192G LEU
193G ASP
5GP F 300
68E LYS
133E GLU
134E ASP
135E ILE
136E ILE
137E ASP
138E THR
139E GLY
140E LYS
141E THR
142E MET
165E LYS
185E LYS
186E PHE
187E VAL
188E VAL
192E LEU
193E ASP
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).

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apo-structure
pdb ID
1z7g Details
other holo-structures
pdb ID Ligand Unique ID
3ggc H26A_218 Details
H26D_218
H26B_218
H26C_218
3ggj 25HB_218 Details
25HD_218
25HC_218
25HA_218
3gep 24HC_218 Details
24HA_218
24HB_218
24HD_218
1bzy IMUQ_300 POPT_400 _MGS_900 _MGR_901 Details
IMUB_300 POPE_400 _MGD_900 _MGC_901
IMUG_300 _MGI_900 _MGH_901 POPJ_400
IMUL_300 _MGN_900 POPO_400 _MGM_901
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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5GP NAME: guanosine-5'-monophosphate
FORMULA: C10 H14 N5 O8 P1
SMILES: NC1=Nc2[n](cnc2C(=O)N1)C3OC(COP(O)(O)=O)C(O)C3O
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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