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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2cwh
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF DELTA1-PIPERIDEINE-2-CARBOXYLATE REDUCTASE FROM PSEUDOMONAS SYRINGAE COMPLEXED WITH NADPH AND PYRROLE-2-CARBOXYLATE TITLE
DELTA1-PIPERIDEINE-2-CARBOXYLATE 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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NDP B2510
51A SER
53A SER
54A HIS
126A HIS
128A ALA
129A ALA
130A LEU
131A TRP
148A VAL
150A SER
157D HIS
158D GLY
166A THR
168A PRO
182A VAL
183A PHE
184A ASP
185A LEU
186A ALA
190A ILE
191A ALA
194A ASP
236D HIS
237D LYS
239D SER
240D ALA
272A PRO
307A GLN
309A ARG
310A LEU
311A PRO
312A GLY
314A ARG
315A ARG
NDP E1510
51D SER
53D SER
54D HIS
126D HIS
128D ALA
129D ALA
130D LEU
131D TRP
148D VAL
150D SER
157A HIS
158A GLY
166D THR
168D PRO
182D VAL
183D PHE
184D ASP
185D LEU
186D ALA
190D ILE
191D ALA
194D ASP
236A HIS
237A LYS
239A SER
240A ALA
272D PRO
307D GLN
309D ARG
310D LEU
311D PRO
312D GLY
314D ARG
315D ARG
PYC C2520
54A HIS
58A ARG
126A HIS
127A PHE
150A SER
151A MET
166A THR
191A ALA
192A HIS
193A GLY
272A PRO
PYC F1520
54D HIS
58D ARG
126D HIS
127D PHE
150D SER
151D MET
166D THR
191D ALA
192D HIS
193D GLY
270D GLN
272D PRO
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
1wtj Details
other holo-structures
pdb ID Ligand Unique ID
2cwf NDPB2510 Details
NDPD1510
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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NDP NAME: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H30 N7 O17 P3
SMILES: NC(=O)C1=CN(C=CC1)C2OC(COP(O)(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
PYC NAME: PYRROLE-2-CARBOXYLATE
FORMULA: C5 H4 N1 O2
SMILES: [O-]C(=O)c1[nH]ccc1
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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