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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2jbs
OXIDOREDUCTASE HEADER
STRUCTURE OF THE MONOOXYGENASE COMPONENT OF P- HYDROXYPHENYLACETATE HYDROXYLASE FROM ACINETOBACTER BAUMANNII TITLE
P-HYDROXYPHENYLACETATE HYDROXYLASE C2\:OXYGENASE 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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FMN H1423
112A TRP
116A LEU
146A SER
147A SER
148A ILE
149A ALA
151A PHE
168A GLY
169A TRP
170A SER
171A SER
210A TRP
215A ILE
218A SER
220A SER
266A PHE
292G ARG
293G VAL
294G ARG
295G ALA
296G TYR
372G ALA
373G GLY
374G ALA
375G THR
392A MET
395A ALA
396A HIS
397A ALA
FMN B1423
112G TRP
116G LEU
120G HIS
146G SER
147G SER
148G ILE
149G ALA
151G PHE
168G GLY
169G TRP
170G SER
171G SER
210G TRP
215G ILE
218G SER
220G SER
266G PHE
270G PHE
292A ARG
293A VAL
294A ARG
295A ALA
296A TYR
372A ALA
373A GLY
374A ALA
375A THR
392G MET
395G ALA
396G HIS
397G ALA
FMN F1423
112C TRP
116C LEU
146C SER
147C SER
148C ILE
149C ALA
151C PHE
168C GLY
169C TRP
170C SER
171C SER
210C TRP
215C ILE
218C SER
220C SER
266C PHE
292E ARG
293E VAL
294E ARG
295E ALA
296E TYR
372E ALA
373E GLY
374E ALA
375E THR
392C MET
395C ALA
396C HIS
397C ALA
FMN D1423
112E TRP
116E LEU
146E SER
147E SER
148E ILE
149E ALA
151E PHE
168E GLY
169E TRP
170E SER
171E SER
210E TRP
215E ILE
220E SER
266E PHE
270E PHE
292C ARG
293C VAL
294C ARG
295C ALA
296C TYR
372C ALA
373C GLY
374C ALA
375C THR
392E MET
395E ALA
396E HIS
397E ALA
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):

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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
2jbr Details
other holo-structures
pdb ID Ligand Unique ID
2jbt 4HPL1424 FMNK1423 Details
4HPI1424 FMNH1423
4HPF1424 FMNE1423
4HPC1424 FMNB1423
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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FMN NAME: FLAVIN MONONUCLEOTIDE
FORMULA: C17 H21 N4 O9 P1
SMILES: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CC(O)C(O)C(O)COP(O)(O)=O)c2cc1C
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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