university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

(click anywhere in this window to remove it)
1rya
HYDROLASE HEADER
CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN COMPLEX WITH GDP AND MG TITLE
GDP-MANNOSE MANNOSYL HYDROLASE 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
GDP B 770
3A PHE
4A LEU
6A GLN
9A PHE
37A ARG
39A ASN
40A ARG
41A PRO
50A GLY
51A GLY
52A ARG
54A GLN
65A ARG
66A LEU
70A GLU
94A PHE
103A TYR
123A GLN
GDP F 771
3E PHE
4E LEU
6E GLN
9E PHE
37E ARG
39E ASN
40E ARG
41E PRO
50E GLY
51E GLY
52E ARG
54E GLN
65E ARG
66E LEU
70E GLU
94E PHE
103E TYR
123E GLN
TRS D 870
20A SER
21A LEU
22A ASP
37A ARG
41A PRO
42A ALA
47A PHE
48A VAL
50A GLY
51A GLY
88A HIS
90A TYR
103A TYR
105A VAL
TRS I 871
20E SER
22E ASP
37E ARG
41E PRO
42E ALA
47E PHE
48E VAL
50E GLY
51E GLY
88E HIS
90E TYR
103E TYR
105E VAL
MG C1001
37A ARG
50A GLY
70A GLU
123A GLN
124A HIS
MG H1002
37E ARG
50E GLY
70E GLU
123E GLN
124E HIS
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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
2gt2 Details
other holo-structures
pdb ID Ligand Unique ID
none
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.

(click anywhere in this window to remove it)
GDP NAME: GUANOSINE-5'-DIPHOSPHATE
FORMULA: C10 H15 N5 O11 P2
SMILES: NC1=Nc2[n](cnc2C(=O)N1)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
TRS NAME: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
FORMULA: C4 H12 N1 O3
SMILES: [NH3+]C(CO)(CO)CO
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
Script execution time: 0.0642 seconds