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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1hj6
OXIDOREDUCTASE HEADER
ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED) TITLE
ISOCITRATE 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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GOL E1417
16A LEU
19A GLY
21A LEU
96A ARG
97A VAL
328A ILE
329A GLY
330A ASP
331A GLU
332A CYS
333A ALA
366A HIS
GOL K1417
16G LEU
19G GLY
21G LEU
96G ARG
97G VAL
328G ILE
329G GLY
330G ASP
331G GLU
332G CYS
333G ALA
366G HIS
NAP H1420
37G ILE
41G VAL
100G LYS
102G PRO
103G LEU
104G THR
105G THR
113G GLU
115G ASN
119G ARG
232A ASN
281A ILE
283A ASP
284A ALA
287A GLN
288A GLN
291A LEU
292A ARG
320G ILE
321G GLY
336G GLU
337G ALA
338G THR
339G HIS
340G GLY
341G THR
342G ALA
343G PRO
344G LYS
345G TYR
351G VAL
352G ASN
391G TYR
392G ASP
NAP B1420
37A ILE
41A VAL
100A LYS
102A PRO
103A LEU
104A THR
105A THR
113A GLU
115A ASN
119A ARG
232G ASN
281G ILE
283G ASP
284G ALA
287G GLN
288G GLN
291G LEU
292G ARG
320A ILE
321A GLY
336A GLU
337A ALA
338A THR
339A HIS
340A GLY
341A THR
342A ALA
343A PRO
344A LYS
345A TYR
351A VAL
352A ASN
391A TYR
392A ASP
IPM J1419
113G GLU
115G ASN
116G VAL
119G ARG
129G ARG
153G ARG
160G TYR
230A LYS
232A ASN
233A ILE
283A ASP
307G ASP
338G THR
IPM D1419
113A GLU
115A ASN
116A VAL
119A ARG
129A ARG
153A ARG
160A TYR
230G LYS
232G ASN
233G ILE
283G ASP
307A ASP
338A THR
GOL F1418
126A ILE
128A LEU
152A PHE
212A ALA
216A TYR
328A ILE
335A PHE
362A MET
366A HIS
GOL L1418
126G ILE
128G LEU
152G PHE
212G ALA
216G TYR
328G ILE
335G PHE
362G MET
366G HIS
MG I1421
129G ARG
283A ASP
307G ASP
311G ASP
338G THR
MG C1421
129A ARG
283G ASP
307A ASP
311A ASP
338A THR
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
7icd 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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GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
IPM NAME: 3-ISOPROPYLMALIC ACID
FORMULA: C7 H12 O5
SMILES: CC(C)C(C(O)C(O)=O)C(O)=O
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
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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