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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1khr
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF VAT(D) IN COMPLEX WITH VIRGINIAMYCIN AND COENZYME A 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.

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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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VIR B 402
11G ILE
14G ASN
16G SER
17G VAL
37G TYR
39G ASP
52A TYR
54A TYR
56A ILE
57A LEU
79A GLY
80A ALA
81A ASN
82A HIS
83A ARG
90A PRO
92A ASN
93A LEU
102A MET
103A PRO
105A LEU
108A LEU
VIR E 401
11A ILE
14A ASN
16A SER
17A VAL
37A TYR
39A ASP
52D TYR
54D TYR
56D ILE
57D LEU
79D GLY
80D ALA
81D ASN
82D HIS
83D ARG
90D PRO
92D ASN
93D LEU
102D MET
103D PRO
105D LEU
108D LEU
COA C 303
37G TYR
39G ASP
52A TYR
68G SER
69G ILE
70G GLY
71G PRO
76A ILE
80A ALA
81A ASN
82A HIS
84A MET
109A PRO
111A LYS
121G TRP
122G ILE
123G GLY
124G LYS
129A MET
130A PRO
139G ILE
140G VAL
141G ALA
142G ALA
144G SER
145A VAL
147A VAL
148A LYS
155G LEU
157G GLY
158G GLY
159A ASN
160A PRO
164G ILE
165G LYS
COA F 301
37A TYR
39A ASP
52D TYR
68A SER
69A ILE
70A GLY
71A PRO
76D ILE
80D ALA
81D ASN
82D HIS
84D MET
109D PRO
121A TRP
122A ILE
123A GLY
124A LYS
129D MET
130D PRO
139A ILE
140A VAL
141A ALA
142A ALA
144A SER
145D VAL
147D VAL
148D LYS
155A LEU
157A GLY
158A GLY
159D ASN
160D PRO
164A ILE
165A LYS
COA H 302
37D TYR
39D ASP
52G TYR
68D SER
69D ILE
70D GLY
71D PRO
76G ILE
80G ALA
81G ASN
82G HIS
84G MET
109G PRO
111G LYS
121D TRP
123D GLY
124D LYS
129G MET
130G PRO
139D ILE
140D VAL
141D ALA
142D ALA
144D SER
145G VAL
147G VAL
148G LYS
155D LEU
157D GLY
158D GLY
159G ASN
160G PRO
164D ILE
165D 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.

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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
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.

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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
1kk4 ACOF_301 Details
ACOB_303
ACOD_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.

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COA NAME: COENZYME A
FORMULA: C21 H36 N7 O16 P3 S1
SMILES: CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)[n]2cnc3c(N)ncnc23)C(O)C(=O)NCCC(=O)NCCS
VIR NAME: VIRGINIAMYCIN M1
FORMULA: C28 H35 N3 O7
SMILES: CC(C)C1OC(=O)C2=CCCN2C(=O)c3coc(CC(=O)CC(O)C=C(C)C=CCNC(=O)C=CC1C)n3
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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