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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2ae2
OXIDOREDUCTASE HEADER
TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE TITLE
PROTEIN (TROPINONE REDUCTASE-II) 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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NAP K 261
16J GLY
18J SER
19J ARG
20J GLY
21J ILE
22J GLY
39J CYS
40J SER
41J ARG
42J ASN
45J GLU
65J CYS
66J ASP
67J LEU
68J SER
94J ASN
95J ALA
96J GLY
97J ILE
117J ILE
144J ILE
145J SER
146J SER
159J TYR
163J LYS
189J PRO
190J GLY
191J VAL
192J ILE
194J THR
195J SER
196J LEU
197J VAL
NAP B 261
16A GLY
18A SER
19A ARG
20A GLY
21A ILE
22A GLY
39A CYS
40A SER
41A ARG
42A ASN
45A GLU
65A CYS
66A ASP
67A LEU
68A SER
94A ASN
95A ALA
96A GLY
97A ILE
117A ILE
144A ILE
145A SER
146A SER
159A TYR
163A LYS
189A PRO
190A GLY
192A ILE
194A THR
195A SER
196A LEU
197A VAL
NAP H 261
16G GLY
18G SER
19G ARG
20G GLY
21G ILE
22G GLY
39G CYS
40G SER
41G ARG
42G ASN
45G GLU
65G CYS
66G ASP
67G LEU
94G ASN
95G ALA
96G GLY
97G ILE
117G ILE
144G ILE
145G SER
146G SER
159G TYR
163G LYS
189G PRO
190G GLY
192G ILE
194G THR
195G SER
196G LEU
197G VAL
NAP E 261
16D GLY
18D SER
19D ARG
20D GLY
21D ILE
22D GLY
39D CYS
40D SER
41D ARG
42D ASN
45D GLU
65D CYS
66D ASP
67D LEU
94D ASN
95D ALA
96D GLY
97D ILE
117D ILE
144D ILE
145D SER
146D SER
159D TYR
163D LYS
189D PRO
190D GLY
192D ILE
194D THR
195D SER
196D LEU
197D VAL
PTO L 262
98J VAL
100J TYR
146J SER
147J VAL
148J SER
153J VAL
156J GLU
159J TYR
190J GLY
191J VAL
196J LEU
197J VAL
200J THR
206J GLN
209J ASN
210J LEU
213J LEU
PTO C 262
98A VAL
100A TYR
146A SER
147A VAL
148A SER
153A VAL
156A GLU
159A TYR
190A GLY
191A VAL
196A LEU
197A VAL
200A THR
206A GLN
209A ASN
210A LEU
213A LEU
PTO I 262
98G VAL
100G TYR
146G SER
147G VAL
148G SER
153G VAL
156G GLU
159G TYR
190G GLY
191G VAL
196G LEU
197G VAL
200G THR
206G GLN
209G ASN
210G LEU
213G LEU
PTO F 262
98D VAL
100D TYR
146D SER
147D VAL
148D SER
153D VAL
156D GLU
159D TYR
190D GLY
191D VAL
196D LEU
197D VAL
200D THR
206D GLN
209D ASN
210D LEU
213D LEU
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).

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apo-structure
pdb ID
2ae1 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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NAP NAME: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H28 N7 O17 P3
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
PTO NAME: PSEUDOTROPINE
FORMULA: C8 H15 N1 O1
SMILES: CN1C2CCC1CC(O)C2
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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