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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holo-structureHelp

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

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2jbt
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
112D TRP
116D LEU
120D HIS
146D SER
147D SER
148D ILE
149D ALA
151D PHE
168D GLY
169D TRP
170D SER
171D SER
210D TRP
215D ILE
220D SER
292G ARG
293G VAL
294G ARG
295G ALA
296G TYR
372G ALA
373G GLY
374G ALA
375G THR
392D MET
395D ALA
396D HIS
397D ALA
FMN B1423
112J TRP
116J LEU
146J SER
147J SER
148J ILE
149J ALA
151J PHE
168J GLY
169J TRP
170J SER
171J SER
210J TRP
215J ILE
220J SER
292A ARG
293A VAL
294A ARG
295A ALA
296A TYR
372A ALA
373A GLY
374A ALA
375A THR
392J MET
395J ALA
396J HIS
397J ALA
FMN K1423
112A TRP
116A LEU
120A HIS
146A SER
147A SER
148A ILE
149A ALA
151A PHE
168A GLY
169A TRP
170A SER
171A SER
210A TRP
215A ILE
220A SER
292J ARG
293J VAL
295J ALA
296J TYR
372J ALA
373J GLY
374J ALA
375J THR
392A MET
395A ALA
396A HIS
397A ALA
FMN E1423
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
220G SER
292D ARG
293D VAL
294D ARG
295D ALA
296D TYR
372D ALA
373D GLY
374D ALA
375D THR
392G MET
395G ALA
396G HIS
397G ALA
4HP L1424
116A LEU
120A HIS
146A SER
148A ILE
262A TYR
263A ARG
266A PHE
267A ALA
270A PHE
296J TYR
396A HIS
398A TYR
4HP I1424
116D LEU
120D HIS
146D SER
148D ILE
262D TYR
263D ARG
266D PHE
267D ALA
270D PHE
296G TYR
396D HIS
398D TYR
4HP F1424
116G LEU
120G HIS
146G SER
148G ILE
262G TYR
263G ARG
266G PHE
267G ALA
270G PHE
296D TYR
396G HIS
398G TYR
4HP C1424
116J LEU
120J HIS
146J SER
148J ILE
262J TYR
263J ARG
266J PHE
267J ALA
270J PHE
296A TYR
396J HIS
398J TYR
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
2jbr Details
other holo-structures
pdb ID Ligand Unique ID
2jbs FMNH1423 Details
FMNB1423
FMNF1423
FMND1423
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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4HP NAME: 4-HYDROXYPHENYLACETATE
FORMULA: C8 H8 O3
SMILES: OC(=O)Cc1ccc(O)cc1
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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