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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1q51
LYASE HEADER
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MENB IN COMPLEX WITH ACETOACETYL-COENZYME A, A KEY ENZYME IN VITAMIN K2 BIOSYNTHESIS TITLE
MENB 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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CAA J 506
56K GLU
57K VAL
58K ARG
60K ALA
61K PHE
95K LYS
96K ASP
103K SER
105K GLY
106K ASP
107K GLN
134K LEU
136K ILE
157K TRP
159K ALA
160K GLY
161K GLY
182K LYS
184K THR
185K ASP
187K ASP
188K VAL
190K SER
299I PHE
302I LYS
CAA H 503
56E GLU
57E VAL
58E ARG
60E ALA
61E PHE
95E LYS
96E ASP
103E SER
105E GLY
106E ASP
107E GLN
134E LEU
136E ILE
157E TRP
159E ALA
160E GLY
161E GLY
182E LYS
184E THR
185E ASP
188E VAL
190E SER
299G PHE
302G LYS
CAA L 502
56I GLU
57I VAL
58I ARG
60I ALA
61I PHE
95I LYS
96I ASP
103I SER
105I GLY
106I ASP
107I GLN
134I LEU
136I ILE
157I TRP
159I ALA
160I GLY
161I GLY
182I LYS
184I THR
185I ASP
188I VAL
190I SER
299K PHE
302K LYS
CAA B 504
56C GLU
57C VAL
58C ARG
60C ALA
61C PHE
95C LYS
96C ASP
103C SER
105C GLY
106C ASP
107C GLN
134C LEU
136C ILE
157C TRP
159C ALA
160C GLY
161C GLY
182C LYS
184C THR
185C ASP
188C VAL
190C SER
299A PHE
302A LYS
CAA F 505
56G GLU
57G VAL
58G ARG
60G ALA
61G PHE
95G LYS
96G ASP
103G SER
105G GLY
106G ASP
107G GLN
134G LEU
136G ILE
157G TRP
159G ALA
160G GLY
161G GLY
182G LYS
184G THR
185G ASP
188G VAL
190G SER
299E PHE
302E LYS
CAA D 501
56A GLU
57A VAL
58A ARG
60A ALA
61A PHE
95A LYS
96A ASP
103A SER
105A GLY
106A ASP
107A GLN
134A LEU
136A ILE
157A TRP
159A ALA
160A GLY
161A GLY
182A LYS
184A THR
185A ASP
188A VAL
190A SER
299C PHE
300C LEU
302C 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:

» 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
1q52 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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CAA NAME: ACETOACETYL-COENZYME A
FORMULA: C25 H40 N7 O18 P3 S1
SMILES: CC(=O)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)[n]2cnc3c(N)ncnc23
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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