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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3ek5
TRANSFERASE HEADER
UNIQUE GTP-BINDING POCKET AND ALLOSTERY OF UMP KINASE FROM A GRAM-NEGATIVE PHYTOPATHOGEN BACTERIUM TITLE
URIDYLATE KINASE 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 H2005
75E HIS
98G LYS
99G VAL
100G ARG
101G VAL
108G ASN
109G ASP
110G VAL
111G CYS
112G GLU
115A ILE
117A ARG
118A ARG
121A ARG
122G HIS
125A LYS
127G ARG
GTP L2003
75I HIS
89K GLN
93K GLU
98K LYS
100K ARG
101K VAL
108K ASN
109K ASP
110K VAL
111K CYS
112K GLU
115C ILE
117C ARG
118K ARG
121C ARG
125C LYS
127K ARG
GTP J2006
89I GLN
98I LYS
99I VAL
100I ARG
101I VAL
108I ASN
109I ASP
110I VAL
111I CYS
112I GLU
115G ILE
117G ARG
118G ARG
121G ARG
125G LYS
127I ARG
GTP D2001
89C GLN
98C LYS
99C VAL
100C ARG
101C VAL
108C ASN
109C ASP
110C VAL
111C CYS
112C GLU
115E ILE
117E ARG
118E ARG
121E ARG
125E LYS
127C ARG
GTP F2002
89E GLN
93E GLU
99E VAL
100E ARG
101E VAL
108E ASN
109E ASP
110E VAL
111E CYS
112E GLU
115K ILE
117K ARG
118E ARG
121K ARG
122K HIS
125K LYS
127E ARG
GTP B2004
98A LYS
100A ARG
101A VAL
108A ASN
109A ASP
110A VAL
111A CYS
112A GLU
115I ILE
117I ARG
118I ARG
121I ARG
122A HIS
125I LYS
127A 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.

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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
3ek6 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.

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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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