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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1mi3
OXIDOREDUCTASE HEADER
1.8 ANGSTROM STRUCTURE OF XYLOSE REDUCTASE FROM CANDIDA TENUIS IN COMPLEX WITH NADH TITLE
XYLOSE 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 D2350
22C GLY
23C CYS
24C TRP
25C LYS
47C ASP
52C TYR
81C LYS
114C HIS
115C PHE
169C SER
170C ASN
191C GLN
217C TYR
218C SER
219C SER
220C PHE
223C GLN
224C SER
225C PHE
227C GLU
240C PHE
257C ALA
272C ILE
273C PRO
274C LYS
276C ASN
280C ARG
283C GLN
284C ASN
310C ASN
NAD H4350
22G GLY
23G CYS
24G TRP
25G LYS
47G ASP
52G TYR
81G LYS
114G HIS
115G PHE
169G SER
170G ASN
191G GLN
217G TYR
218G SER
219G SER
220G PHE
221G GLY
223G GLN
224G SER
225G PHE
227G GLU
240G PHE
257G ALA
272G ILE
273G PRO
274G LYS
276G ASN
280G ARG
283G GLN
284G ASN
310G ASN
NAD F3350
22E GLY
23E CYS
24E TRP
25E LYS
47E ASP
52E TYR
81E LYS
114E HIS
115E PHE
169E SER
170E ASN
191E GLN
217E TYR
218E SER
219E SER
220E PHE
223E GLN
224E SER
225E PHE
226A VAL
227E GLU
229A ASN
240E PHE
257E ALA
272E ILE
273E PRO
274E LYS
276E ASN
280E ARG
283E GLN
284E ASN
310E ASN
NAD B1350
22A GLY
23A CYS
24A TRP
25A LYS
47A ASP
52A TYR
81A LYS
114A HIS
115A PHE
169A SER
170A ASN
191A GLN
217A TYR
218A SER
219A SER
220A PHE
221A GLY
223A GLN
224A SER
225A PHE
226E VAL
227E GLU
229E ASN
240A PHE
255A THR
257A ALA
258A GLU
272A ILE
273A PRO
274A LYS
275A SER
276A ASN
280A ARG
283A GLN
284A ASN
310A ASN
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
1jez Details
other holo-structures
pdb ID Ligand Unique ID
1k8c NAPH4350 Details
NAPD2350
NAPF3350
NAPB1350
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
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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