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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1l3i
TRANSFERASE, LYASE HEADER
MT0146, THE PRECORRIN-6Y METHYLTRANSFERASE (CBIT) HOMOLOG FROM M. THERMOAUTOTROPHICUM, ADOHCY BINARY COMPLEX TITLE
PRECORRIN-6Y METHYLTRANSFERASE/PUTATIVE 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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SAH D 804
13D VAL
14D PRO
15D GLY
16D PRO
17D THR
39D ASP
41D GLY
42D CYS
43D GLY
44D THR
45D GLY
46D GLY
47D VAL
61D ILE
62D ASP
63D ARG
64D ASN
67D ALA
89D GLY
90D ASP
91D ALA
107D GLY
108D GLY
109D SER
110D GLY
112D GLU
116D ILE
SAH A 801
13A VAL
14A PRO
15A GLY
16A PRO
17A THR
39A ASP
41A GLY
42A CYS
43A GLY
44A THR
45A GLY
46A GLY
47A VAL
61A ILE
62A ASP
63A ARG
64A ASN
67A ALA
89A GLY
90A ASP
91A ALA
107A GLY
108A GLY
109A SER
110A GLY
112A GLU
116A ILE
133A THR
SAH C 803
13C VAL
14C PRO
15C GLY
16C PRO
17C THR
39C ASP
41C GLY
42C CYS
43C GLY
44C THR
45C GLY
46C GLY
47C VAL
61C ILE
62C ASP
63C ARG
64C ASN
67C ALA
89C GLY
91C ALA
107C GLY
108C GLY
109C SER
110C GLY
112C GLU
116C ILE
133C THR
169B ARG
SAH B 802
13B VAL
14B PRO
15B GLY
16B PRO
17B THR
39B ASP
41B GLY
42B CYS
43B GLY
44B THR
45B GLY
46B GLY
47B VAL
61B ILE
62B ASP
63B ARG
64B ASN
67B ALA
89B GLY
90B ASP
91B ALA
107B GLY
108B GLY
109B SER
110B GLY
112B GLU
116B ILE
133B THR
169C 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).

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apo-structure
pdb ID
1f38 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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SAH NAME: S-ADENOSYL-L-HOMOCYSTEINE
FORMULA: C14 H20 N6 O5 S1
SMILES: NC(CCSCC1OC(C(O)C1O)[n]2cnc3c(N)ncnc23)C(O)=O
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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