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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2wyw
OXIDOREDUCTASE HEADER
HIGH RESOLUTION STRUCTURE OF THERMUS THERMOPHILUS ENOYL- ACYL CARRIER PROTEIN REDUCTASE NAD AND TRICLOSAN-FORM TITLE
ENOYL-[ACYL CARRIER PROTEIN] REDUCTASE 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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NAD C1260
15A GLY
16A VAL
17A THR
21A SER
22A LEU
23A GLY
41A TYR
42A GLN
46A LEU
65A ALA
66A ASP
67A VAL
68A THR
92A HIS
93A ALA
94A ILE
95A ALA
96A PHE
120A VAL
145A LEU
146A THR
147A TYR
164A LYS
190A ALA
191A GLY
192A PRO
193A VAL
195A THR
196A VAL
197A ALA
NAD L1259
15J GLY
16J VAL
17J THR
18J ASN
21J SER
22J LEU
41J TYR
42J GLN
46J LEU
65J ALA
66J ASP
67J VAL
68J THR
92J HIS
93J ALA
94J ILE
95J ALA
96J PHE
120J VAL
145J LEU
146J THR
147J TYR
164J LYS
190J ALA
191J GLY
192J PRO
193J VAL
195J THR
196J VAL
197J ALA
NAD F1259
15D GLY
16D VAL
17D THR
18D ASN
21D SER
22D LEU
41D TYR
42D GLN
46D LEU
65D ALA
66D ASP
67D VAL
68D THR
92D HIS
93D ALA
94D ILE
95D ALA
96D PHE
120D VAL
145D LEU
146D THR
147D TYR
164D LYS
190D ALA
191D GLY
192D PRO
193D VAL
195D THR
196D VAL
197D ALA
NAD I1259
15G GLY
16G VAL
17G THR
18G ASN
21G SER
22G LEU
41G TYR
42G GLN
46G LEU
65G ALA
66G ASP
67G VAL
68G THR
92G HIS
93G ALA
94G ILE
95G ALA
96G PHE
120G VAL
144G THR
145G LEU
146G THR
147G TYR
164G LYS
190G ALA
191G GLY
192G PRO
193G VAL
195G THR
196G VAL
197G ALA
TCL B1261
95A ALA
96A PHE
97A ALA
102A MET
147A TYR
157A TYR
160A MET
164A LYS
192A PRO
197A ALA
198A ALA
200A SER
201A ILE
204A PHE
207A MET
TCL K1260
95J ALA
96J PHE
97J ALA
102J MET
147J TYR
157J TYR
160J MET
164J LYS
192J PRO
197J ALA
198J ALA
200J SER
201J ILE
204J PHE
207J MET
TCL E1260
95D ALA
96D PHE
97D ALA
102D MET
147D TYR
157D TYR
160D MET
164D LYS
192D PRO
197D ALA
198D ALA
200D SER
201D ILE
204D PHE
207D MET
TCL H1260
95G ALA
96G PHE
97G ALA
102G MET
147G TYR
157G TYR
160G MET
164G LYS
192G PRO
197G ALA
198G ALA
200G SER
201G ILE
204G PHE
207G MET
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
1ulu Details
other holo-structures
pdb ID Ligand Unique ID
2yw9 NAPE_501 Details
2wyv NADI1258 Details
NADD1260
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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NAD NAME: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
FORMULA: C21 H27 N7 O14 P2
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
TCL NAME: TRICLOSAN
FORMULA: C12 H7 O2 CL3
SMILES: Oc1cc(Cl)ccc1Oc2ccc(Cl)cc2Cl
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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