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)
1kk4
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF VAT(D) IN COMPLEX WITH ACETYL-COA TITLE
STREPTOGRAMIN A ACETYLTRANSFERASE 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)
ACO B 303
37C TYR
39C ASP
52A TYR
68C SER
69C ILE
70C GLY
71C PRO
76A ILE
80A ALA
81A ASN
82A HIS
84A MET
109A PRO
111A LYS
121C TRP
122C ILE
123C GLY
124C LYS
129A MET
130A PRO
139C ILE
140C VAL
141C ALA
142C ALA
144C SER
145A VAL
147A VAL
148A LYS
155C LEU
157C GLY
158C GLY
159A ASN
160A PRO
164C ILE
165C LYS
ACO F 301
37A TYR
39A ASP
52E TYR
69A ILE
70A GLY
71A PRO
76E ILE
80E ALA
81E ASN
82E HIS
84E MET
109E PRO
111E LYS
121A TRP
122A ILE
123A GLY
124A LYS
129E MET
130E PRO
139A ILE
140A VAL
141A ALA
142A ALA
144A SER
145E VAL
147E VAL
148E LYS
155A LEU
157A GLY
158A GLY
159E ASN
160E PRO
162A ASN
164A ILE
165A LYS
ACO D 302
37E TYR
39E ASP
52C TYR
68E SER
69E ILE
70E GLY
71E PRO
76C ILE
80C ALA
81C ASN
82C HIS
84C MET
109C PRO
111C LYS
121E TRP
122E ILE
123E GLY
124E LYS
129C MET
130C PRO
139E ILE
140E VAL
141E ALA
142E ALA
144E SER
145C VAL
147C VAL
148C LYS
155E LEU
157E GLY
158E GLY
159C ASN
160C PRO
162E ASN
164E ILE
165E LYS
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
1mr7 Details
other holo-structures
pdb ID Ligand Unique ID
1mrl DOLF_301 Details
DOLD_300
DOLB_302
3dho B2MC_304 Details
B2MC_303
B2MA_305
1mr9 ACOD_304 Details
ACOB_303
ACOF_305
1khr COAC_303 VIRB_402 Details
COAF_301 VIRE_401
COAH_302
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)
ACO NAME: ACETYL COENZYME *A
FORMULA: C23 H38 N7 O17 P3 S1
SMILES: CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)[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
Script execution time: 0.2862 seconds