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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1yr8
HYDROLASE HEADER
PAB0955 CRYSTAL STRUCTURE : A GTPASE IN GTP BOUND FORM FROM PYROCOCCUS ABYSSI TITLE
ATP(GTP)BINDING PROTEIN 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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GTP B 401
8A THR
9A ALA
10A GLY
11A SER
12A GLY
13A LYS
14A THR
15A THR
36A ASP
39A VAL
67C ASN
71C VAL
104A GLY
165A ASN
166A LYS
168A ASP
169A LEU
223A SER
224A ALA
225A LYS
GTP D 401
8C THR
9C ALA
10C GLY
11C SER
12C GLY
13C LYS
14C THR
15C THR
36C ASP
39C VAL
67A ASN
68A GLY
71A VAL
104C GLY
165C ASN
166C LYS
168C ASP
169C LEU
223C SER
224C ALA
225C 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
1yr6 Details
other holo-structures
pdb ID Ligand Unique ID
1yra GDPB_401 Details
GDPD_402
1yr7 GSPB_401 Details
GSPD_401
1yrb GDPE_402 _MGF_502 Details
GDPB_401 _MGC_501
2oxr GDPE_502 _MGF_501 Details
GDPB_502 _MGC_501
1yr9 GDPE_401 Details
GDPB_401
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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GTP NAME: GUANOSINE-5'-TRIPHOSPHATE
FORMULA: C10 H16 N5 O14 P3
SMILES: NC1=Nc2[n](cnc2C(=O)N1)C3OC(COP(O)(=O)OP(O)(=O)OP(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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