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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1lua
OXIDOREDUCTASE HEADER
STRUCTURE OF METHYLENE-TETRAHYDROMETHANOPTERIN DEHYDROGENASE FROM METHYLOBACTERIUM EXTORQUENS AM1 COMPLEXED WITH NADP TITLE
METHYLENE TETRAHYDROMETHANOPTERIN 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 D1456
18C PHE
97C ASN
98C GLY
99C SER
102C THR
127C ALA
129C THR
130C GLY
131C PRO
132C VAL
133C GLY
151C GLY
152C ARG
153C LYS
156C LYS
157C ALA
183C ARG
196C ALA
197C GLY
198C ALA
199C ILE
201C LEU
203C LEU
221C TYR
222C ASN
223C ALA
253C GLY
256C LYS
NAP F2456
18E PHE
97E ASN
98E GLY
99E SER
102E THR
127E ALA
129E THR
130E GLY
131E PRO
132E VAL
133E GLY
151E GLY
152E ARG
153E LYS
156E LYS
183E ARG
196E ALA
197E GLY
198E ALA
199E ILE
201E LEU
203E LEU
221E TYR
222E ASN
223E ALA
253E GLY
256E LYS
NAP B 456
18A PHE
97A ASN
98A GLY
99A SER
102A THR
127A ALA
129A THR
130A GLY
131A PRO
132A VAL
133A GLY
151A GLY
152A ARG
153A LYS
156A LYS
183A ARG
196A ALA
197A GLY
198A ALA
199A ILE
201A LEU
203A LEU
221A TYR
222A ASN
223A ALA
253A GLY
256A LYS
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
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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
1lu9 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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