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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3ku1
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE SP1610, A PUTATIVE TRNA (M1A22) METHYLTRANSFERASE, IN COMPLEX WITH S- ADENOSYL-L-METHIONINE TITLE
SAM-DEPENDENT METHYLTRANSFERASE 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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SAM H 226
5H ARG
6H LEU
21H ASP
22H VAL
23H GLY
24H SER
25H ASP
29H LEU
45H GLY
46H GLU
47H VAL
48H VAL
51H PRO
73H ALA
74H ASN
75H GLY
91H ALA
92H GLY
93H MET
97H LEU
101H ILE
120H ASN
SAM G 226
5G ARG
6G LEU
21G ASP
22G VAL
23G GLY
24G SER
25G ASP
29G LEU
45G GLY
46G GLU
47G VAL
48G VAL
51G PRO
73G ALA
74G ASN
75G GLY
91G ALA
92G GLY
93G MET
97G LEU
101G ILE
120G ASN
SAM C 226
5C ARG
6C LEU
15D GLN
21C ASP
22C VAL
23C GLY
24C SER
25C ASP
29C LEU
32D GLU
36D ARG
37D GLY
38D GLN
45C GLY
46C GLU
47C VAL
48C VAL
51C PRO
73C ALA
74C ASN
75C GLY
91C ALA
92C GLY
93C MET
97C LEU
100C ARG
101C ILE
120C ASN
SAM A 226
5A ARG
6A LEU
15B GLN
21A ASP
22A VAL
23A GLY
24A SER
25A ASP
29A LEU
32B GLU
36B ARG
37B GLY
38B GLN
45A GLY
46A GLU
47A VAL
48A VAL
51A PRO
73A ALA
74A ASN
75A GLY
91A ALA
92A GLY
93A MET
97A LEU
101A ILE
120A ASN
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
3kr9 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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SAM NAME: S-ADENOSYLMETHIONINE
FORMULA: C15 H22 N6 O5 S1
SMILES: C[S+](CCC(N)C([O-])=O)CC1OC(C(O)C1O)[n]2cnc3c(N)ncnc23
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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