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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2fwp
LYASE HEADER
STRUCTURE OF PURE (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE) H59N FROM THE ACIDOPHILIC BACTERIUM ACETOBACTER ACETI, BOUND TO ISOCAIR TITLE
N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE 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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ICR V1001
29U GLY
30U SER
32U SER
33U ASP
56U VAL
57U SER
58U ALA
59U ASN
60U ARG
84U ALA
85U GLY
86U GLY
87U ALA
88U ALA
89U HIS
90U LEU
107U VAL
109U SER
ICR Z1001
29Y GLY
30Y SER
32Y SER
33Y ASP
56Y VAL
57Y SER
58Y ALA
59Y ASN
60Y ARG
84Y ALA
85Y GLY
86Y GLY
87Y ALA
88Y ALA
89Y HIS
90Y LEU
107Y VAL
109Y SER
125S PRO
126S GLY
138Q SER
ICR J1001
29I GLY
30I SER
32I SER
33I ASP
56I VAL
57I SER
58I ALA
59I ASN
60I ARG
84I ALA
85I GLY
86I GLY
87I ALA
88I ALA
89I HIS
90I LEU
107I VAL
109I SER
ICR N1001
29M GLY
30M SER
32M SER
33M ASP
56M VAL
57M SER
58M ALA
59M ASN
60M ARG
84M ALA
85M GLY
86M GLY
87M ALA
88M ALA
89M HIS
90M LEU
107M VAL
109M SER
125K PRO
126K GLY
138I SER
ICR R1001
29Q GLY
30Q SER
32Q SER
33Q ASP
56Q VAL
57Q SER
58Q ALA
59Q ASN
60Q ARG
84Q ALA
85Q GLY
86Q GLY
87Q ALA
88Q ALA
89Q HIS
90Q LEU
107Q VAL
109Q SER
125W PRO
126W GLY
138U SER
ICR F1001
123O GLN
125O PRO
126O GLY
138M SER
ICR B1001
125G PRO
126G GLY
ICR D1001
138Y 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).

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apo-structure
pdb ID
2fw7 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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ICR NAME: (4R)-5-IMINO-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-4,5-DIHYDRO-1H-IMIDAZOLE-4-CARBOXYLIC ACID
FORMULA: C9 H14 N3 O9 P1
SMILES: OC1C(O)C(OC1COP(O)(O)=O)N2C=NC(C(O)=O)C2=N
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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