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)
2ate
LYASE HEADER
STRUCTURE OF THE COMPLEX OF PURE WITH NITROAIR TITLE
PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE 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)
NIA L 400
15K GLY
16K SER
17K LYS
18K SER
19K ASP
43K SER
44K ALA
45K HIS
46K ARG
70K ALA
71K GLY
73K ALA
74K ALA
75K HIS
76K LEU
93K VAL
111M PRO
112M ARG
NIA N 400
15M GLY
16M SER
17M LYS
18M SER
19M ASP
43M SER
44M ALA
45M HIS
46M ARG
70M ALA
71M GLY
73M ALA
74M ALA
75M HIS
76M LEU
93M VAL
111K PRO
112K ARG
NIA B 400
15A GLY
16A SER
17A LYS
18A SER
19A ASP
43A SER
44A ALA
45A HIS
46A ARG
70A ALA
71A GLY
73A ALA
74A ALA
75A HIS
76A LEU
93A VAL
111G PRO
112G ARG
NIA D 400
15C GLY
16C SER
17C LYS
18C SER
19C ASP
43C SER
44C ALA
45C HIS
46C ARG
70C ALA
71C GLY
73C ALA
74C ALA
75C HIS
76C LEU
93C VAL
111I PRO
112I ARG
NIA J 400
15I GLY
16I SER
17I LYS
18I SER
19I ASP
43I SER
44I ALA
45I HIS
46I ARG
70I ALA
71I GLY
73I ALA
74I ALA
75I HIS
76I LEU
93I VAL
111C PRO
112C ARG
NIA F 400
15E GLY
16E SER
17E LYS
18E SER
19E ASP
43E SER
44E ALA
45E HIS
46E ARG
70E ALA
71E GLY
73E ALA
74E ALA
75E HIS
76E LEU
93E VAL
111O PRO
112O ARG
NIA H 400
15G GLY
16G SER
17G LYS
18G SER
19G ASP
43G SER
44G ALA
45G HIS
46G ARG
70G ALA
71G GLY
73G ALA
74G ALA
75G HIS
76G LEU
93G VAL
111A PRO
112A ARG
NIA P 400
15O GLY
16O SER
17O LYS
18O SER
19O ASP
43O SER
44O ALA
45O HIS
46O ARG
70O ALA
71O GLY
73O ALA
74O ALA
75O HIS
76O LEU
93O VAL
111E PRO
112E ARG
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
1qcz 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)
NIA NAME: not_found
FORMULA: not_found
SMILES: not_found
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: 0.0737 seconds