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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2cvq
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF NAD(H)-DEPENDENT MALATE DEHYDROGENASE COMPLEXED WITH NADPH TITLE
MALATE DEHYDROGENASE 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 B 334
10A GLY
12A ALA
13A GLY
14A GLN
15A ILE
16A GLY
41A GLU
42A ILE
45A ALA
86A VAL
87A GLY
88A ALA
89A ALA
90A PRO
91A ARG
128A VAL
129A GLY
130A ASN
154A MET
157A LEU
161A ARG
240A SER
241A SER
242A ALA
245A ALA
NAP F1334
10E GLY
12E ALA
13E GLY
14E GLN
15E ILE
41E GLU
42E ILE
45E ALA
86E VAL
87E GLY
88E ALA
89E ALA
90E PRO
91E ARG
128E VAL
129E GLY
130E ASN
154E MET
157E LEU
161E ARG
240E SER
241E SER
245E ALA
TRS D4617
130A ASN
161A ARG
230A GLY
231A ALA
234A ILE
240A SER
241A SER
TRS C4619
130A ASN
132A ALA
154A MET
157A LEU
158A ASP
161A ARG
186A HIS
187A SER
190A MET
226A VAL
227A ALA
230A GLY
TRS G4623
130E ASN
132E ALA
154E MET
157E LEU
158E ASP
161E ARG
186E HIS
187E SER
190E MET
226E VAL
227E ALA
230E GLY
TRS H4621
130E ASN
230E GLY
231E ALA
234E ILE
240E SER
241E SER
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
1iz9 Details
other holo-structures
pdb ID Ligand Unique ID
1y7t NDPF2334 TRSH2335 TRSG2336 Details
NDPB1334 TRSD1335 TRSC1336
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
TRS NAME: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
FORMULA: C4 H12 N1 O3
SMILES: [NH3+]C(CO)(CO)CO
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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