university lille north of france LigASite database of binding sites
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LigASite v9.6 (nr25) - non-redundant
LigASite v9.6 (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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1mbz
HYDROLASE HEADER
BETA-LACTAM SYNTHETASE WITH TRAPPED INTERMEDIATE TITLE
BETA-LACTAM SYNTHETASE 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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IOT H 603
247G VAL
248G LEU
249G SER
254G SER
271G VAL
272G SER
273G MET
280G GLU
323G ILE
326G TYR
329G PRO
330G LEU
333G LEU
346G THR
347G GLY
348G TYR
349G GLY
351G ASP
352G ILE
357G MET
373G ASP
376G THR
377G PHE
380G LEU
382G GLU
443G LYS
IOT B 606
247A VAL
248A LEU
249A SER
254A SER
271A VAL
272A SER
273A MET
280A GLU
323A ILE
326A TYR
330A LEU
333A LEU
346A THR
347A GLY
348A TYR
349A GLY
351A ASP
352A ILE
357A MET
358A HIS
373A ASP
376A THR
377A PHE
380A LEU
382A GLU
443A LYS
444A LEU
445A GLY
446A VAL
447A HIS
449A GLY
450A SER
POP I 604
249G SER
251G GLY
252G ILE
253G ASP
254G SER
347G GLY
351G ASP
423G LYS
427G ARG
441G ARG
442G PRO
443G LYS
444G LEU
MG K 602
249G SER
251G GLY
280G GLU
443G LYS
444G LEU
MG E 604
249A SER
251A GLY
280A GLU
444A LEU
POP D 605
249A SER
251A GLY
252A ILE
253A ASP
254A SER
423A LYS
427A ARG
441A ARG
442A PRO
443A LYS
444A LEU
MG C 603
253A ASP
347A GLY
351A ASP
MG J 601
253G ASP
347G GLY
351G ASP
GOL L 605
273G MET
274G GLY
275G THR
277G THR
278G SER
279G ASN
280G GLU
305G LEU
329G PRO
455G SER
GOL F 607
320A ASP
322A ASP
323A ILE
326A TYR
357A MET
358A HIS
373A ASP
376A THR
380A LEU
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
1m1z Details
other holo-structures
pdb ID Ligand Unique ID
1mb9 ATPB_701 _MGD_604 _MGC_603 Details
ATPH_702 _MGI_602 _MGJ_601
1mc1 AMPH_705 PCXL_706 _MGI_602 POPJ_704 _MGK_605 Details
AMPB_702 POPC_701 _MGD_603 _MGE_601 PCXF_703
1jgt APCB_801 CMAA_803 _MGC_902 Details
APCE_802 _MGF_901 CMAD_804
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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GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
POP NAME: PYROPHOSPHATE 2-
FORMULA: H2 O7 P2
SMILES: OP([O-])(=O)OP(O)([O-])=O
IOT NAME: ARGININE-N-METHYLCARBONYL PHOSPHORIC ACID 5'-ADENOSINE ESTER
FORMULA: C18 H28 N9 O10 P1
SMILES: NC(=N)NCCCC(NCC(=O)OP(O)(=O)OCC1OC(C(O)C1O)[n]2cnc3c(N)ncnc23)C(O)=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
v9.6
January 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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