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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2z09
STRUCTURAL GENOMICS, UNKNOWN FUNCTION HEADER
CRYSTAL STRUCTURE OF UNCHARACTERIZED CONSERVED PROTEIN FROM THERMUS THERMOPHILUS HB8 TITLE
UNIVERSAL STRESS PROTEIN FAMILY 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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ACP E2001
8D ALA
9D TYR
10D ASP
12D SER
15D ALA
36D VAL
37D HIS
38D ALA
58D ARG
87D PRO
91D ILE
105D MET
106D GLY
107D THR
108D ARG
109D GLY
111D GLY
112D ALA
116D LEU
119D GLY
120J SER
121D GLN
122D SER
124J ARG
ACP K2001
8J ALA
9J TYR
10J ASP
12J SER
15J ALA
36J VAL
37J HIS
38J ALA
58J ARG
87J PRO
91J ILE
105J MET
106J GLY
107J THR
108J ARG
109J GLY
110J LEU
111J GLY
112J ALA
116J LEU
119J GLY
120D SER
121J GLN
122J SER
124D ARG
ACP B2001
8A ALA
9A TYR
10A ASP
12A SER
15A ALA
36A VAL
37A HIS
38A ALA
58A ARG
87A PRO
91A ILE
105A MET
106A GLY
107A THR
108A ARG
109A GLY
110A LEU
111A GLY
112A ALA
116A LEU
119A GLY
120G SER
121A GLN
122A SER
124G ARG
ACP H2001
8G ALA
9G TYR
10G ASP
12G SER
15G ALA
36G VAL
37G HIS
38G ALA
58G ARG
87G PRO
91G ILE
105G MET
106G GLY
107G THR
108G ARG
109G GLY
111G GLY
112G ALA
116G LEU
119G GLY
120A SER
121G GLN
122G SER
124A ARG
MG L3001
10J ASP
110J LEU
111J GLY
121J GLN
MG F3001
10D ASP
110D LEU
111D GLY
121D GLN
MG C3001
10A ASP
110A LEU
111A GLY
121A GLN
MG I3001
10G ASP
110G LEU
111G GLY
121G GLN
MG N3002
120D SER
121D GLN
MG M3002
120G SER
121G GLN
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
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.

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apo-structure
pdb ID
1wjg Details
other holo-structures
pdb ID Ligand Unique ID
2z08 ATPH1001 _MGI2001 Details
ATPK1001 _MGL2001
ATPE1001 _MGF2001
ATPB1001 _MGC2001
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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ACP NAME: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
FORMULA: C11 H18 N5 O12 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)CP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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