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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2wvg
LYASE HEADER
STRUCTURAL INSIGHTS INTO THE PRE-REACTION STATE OF PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS TITLE
PYRUVATE DECARBOXYLASE 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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TPU A 600
24D VAL
25D ALA
26D GLY
50D GLU
72D THR
75D VAL
114D HIS
388A THR
389A GLY
390A ASP
391A SER
413A GLY
414A HIS
415A ILE
439A GLY
440A ASP
441A GLY
442A SER
445A LEU
465A ILE
467A ASN
469A GLY
470A TYR
471A THR
472A ILE
473A GLU
TPU G 600
24J VAL
25J ALA
26J GLY
50J GLU
72J THR
75J VAL
114J HIS
388G THR
389G GLY
390G ASP
391G SER
413G GLY
414G HIS
415G ILE
439G GLY
440G ASP
441G GLY
442G SER
445G LEU
465G ILE
467G ASN
469G GLY
470G TYR
471G THR
472G ILE
473G GLU
TPU J 600
24G VAL
25G ALA
26G GLY
50G GLU
72G THR
75G VAL
114G HIS
388J THR
389J GLY
390J ASP
391J SER
413J GLY
414J HIS
415J ILE
439J GLY
440J ASP
441J GLY
442J SER
445J LEU
465J ILE
467J ASN
469J GLY
470J TYR
471J THR
472J ILE
473J GLU
TPU D 600
24A VAL
25A ALA
26A GLY
50A GLU
72A THR
75A VAL
114A HIS
388D THR
389D GLY
390D ASP
391D SER
413D GLY
414D HIS
415D ILE
439D GLY
440D ASP
441D GLY
442D SER
445D LEU
465D ILE
467D ASN
469D GLY
470D TYR
471D THR
472D ILE
473D GLU
F I 570
26J GLY
27J ASP
72J THR
114J HIS
F F 569
26A GLY
27A ASP
72A THR
114A HIS
F C 569
26D GLY
27D ASP
72D THR
114D HIS
MG H 601
439G GLY
440G ASP
465G ILE
467G ASN
469G GLY
MG E 601
439D GLY
440D ASP
465D ILE
467D ASN
469D GLY
MG B 601
440A ASP
465A ILE
467A ASN
469A GLY
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
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
2wvh Details
other holo-structures
pdb ID Ligand Unique ID
2wva PYRD_602 TPUA_600 Details
PYRB_602 TPUC_600
TPUF_600
TPUE_600
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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TPU NAME: not_found
FORMULA: not_found
SMILES: not_found
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
F NAME: FLUORIDE ION
FORMULA: F1
SMILES: [F-]
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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