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)
1jyl
TRANSFERASE HEADER
CATALYTIC MECHANISM OF CTP:PHOSPHOCHOLINE CYTIDYLYTRANSFERASE FROM STREPTOCOCCUS PNEUMONIAE (LICC) TITLE
CTP:PHOSPHOCHOLINE CYTIDYLYTRANSFERASE 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)
CDC D4991
11D LEU
12D ALA
13D ALA
14D GLY
21C PRO
24C GLU
25C ASN
28D LYS
57D ILE
79D ASN
82D TYR
85D TYR
86D ASN
87D ASN
90D SER
105D ASP
106D ALA
107D ASP
135D GLU
136D TRP
159D LEU
190D TYR
192D ASP
216D GLU
218D ASP
CDC C3991
11C LEU
12C ALA
13C ALA
14C GLY
18C ARG
28C LYS
57C ILE
79C ASN
82C TYR
85C TYR
86C ASN
87C ASN
90C SER
105C ASP
106C ALA
107C ASP
135C GLU
136C TRP
159C LEU
161C GLY
190C TYR
192C ASP
216C GLU
218C ASP
CDC B2991
11B LEU
12B ALA
13B ALA
14B GLY
16B GLY
21A PRO
24A GLU
25A ASN
28B LYS
57B ILE
79B ASN
82B TYR
85B TYR
86B ASN
87B ASN
90B SER
105B ASP
106B ALA
107B ASP
135B GLU
136B TRP
159B LEU
190B TYR
192B ASP
216B GLU
218B ASP
CDC A1991
11A LEU
12A ALA
13A ALA
14A GLY
28A LYS
57A ILE
79A ASN
82A TYR
85A TYR
86A ASN
87A ASN
90A SER
105A ASP
106A ALA
107A ASP
135A GLU
136A TRP
159A LEU
190A TYR
192A ASP
216A GLU
218A ASP
MG D4996
105D ASP
107D ASP
216D GLU
218D ASP
MG C3996
105C ASP
107C ASP
216C GLU
218C ASP
MG B2996
105B ASP
107B ASP
216B GLU
218B ASP
MG A1996
105A ASP
107A ASP
216A GLU
218A ASP
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
1jyk 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)
CDC NAME: [2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM
FORMULA: C14 H26 N4 O11 P2
SMILES: C[N+](C)(C)CCOP([O-])(=O)OP(O)(=O)OCC1OC(C(O)C1O)N2C=CC(=NC2=O)N
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
Script execution time: 0.0672 seconds