university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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3afn
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF ALDOSE REDUCTASE A1-R COMPLEXED WITH NA TITLE
MOL_ID: 1; MOLECULE: A1-R, 4-DEOXY-L-ERYTHRO-5-HEXOSEULOSE-URONIC ACID REDUCTASE; CHAIN: B, A, C, D; EC: 1.1.1.126; ENGINEERED: YES 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 K3001
14J GLY
16J SER
17J GLN
18J GLY
19J ILE
37J HIS
38J GLY
39J ARG
40J LYS
64J ALA
65J ASP
66J LEU
67J ALA
92J ASN
93J ALA
94J GLY
95J GLY
116J ALA
148J THR
149J GLY
150J SER
164J TYR
168J LYS
194J PRO
195J GLY
197J VAL
199J THR
200J ALA
201J PHE
202J HIS
NAP B3001
14A GLY
16A SER
17A GLN
18A GLY
19A ILE
37A HIS
38A GLY
39A ARG
40A LYS
64A ALA
65A ASP
66A LEU
67A ALA
92A ASN
93A ALA
94A GLY
95A GLY
116A ALA
148A THR
149A GLY
150A SER
164A TYR
168A LYS
194A PRO
195A GLY
197A VAL
199A THR
200A ALA
201A PHE
202A HIS
NAP H3001
14G GLY
16G SER
17G GLN
18G GLY
19G ILE
37G HIS
38G GLY
39G ARG
40G LYS
64G ALA
65G ASP
66G LEU
67G ALA
92G ASN
93G ALA
94G GLY
95G GLY
116G ALA
148G THR
149G GLY
150G SER
164G TYR
168G LYS
194G PRO
195G GLY
197G VAL
199G THR
200G ALA
201G PHE
202G HIS
NAP E3001
14D GLY
16D SER
17D GLN
18D GLY
19D ILE
20D GLY
37D HIS
38D GLY
39D ARG
40D LYS
64D ALA
65D ASP
66D LEU
67D ALA
92D ASN
93D ALA
94D GLY
95D GLY
116D ALA
148D THR
149D GLY
150D SER
151D ILE
164D TYR
168D LYS
194D PRO
195D GLY
197D VAL
199D THR
200D ALA
201D PHE
202D HIS
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
Hide table of related structures
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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
3afm 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
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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