university lille north of france LigASite database of binding sites
holo-structureHelp

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

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1jgt
HYDROLASE HEADER
CRYSTAL STRUCTURE OF BETA-LACTAM SYNTHETASE 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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APC B 801
247A VAL
248A LEU
249A SER
251A GLY
252A ILE
253A ASP
254A SER
271A VAL
272A SER
273A MET
280A GLU
329A PRO
330A LEU
333A LEU
346A THR
347A GLY
348A TYR
351A ASP
423A LYS
427A ARG
443A LYS
APC E 802
247D VAL
248D LEU
249D SER
251D GLY
252D ILE
253D ASP
254D SER
271D VAL
272D SER
273D MET
280D GLU
326D TYR
329D PRO
330D LEU
333D LEU
346D THR
347D GLY
348D TYR
351D ASP
423D LYS
427D ARG
443D LYS
444D LEU
MG C 902
253A ASP
347A GLY
351A ASP
MG F 901
253D ASP
347D GLY
351D ASP
CMA A 803
323A ILE
326A TYR
329A PRO
330A LEU
348A TYR
349A GLY
351A ASP
352A ILE
357A MET
373A ASP
377A PHE
380A LEU
382A GLU
443A LYS
CMA D 804
323D ILE
326D TYR
348D TYR
349D GLY
351D ASP
352D ILE
357D MET
373D ASP
376D THR
377D PHE
380D LEU
382D GLU
443D 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:

LigPlot (hosted at the EBI):

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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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).

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apo-structure
pdb ID
1m1z Details
other holo-structures
pdb ID Ligand Unique ID
1mbz GOLL_605 POPI_604 IOTH_603 _MGK_602 _MGJ_601 Details
GOLF_607 IOTB_606 _MGE_604 POPD_605 _MGC_603
POPI_604 IOTH_603 _MGK_602 _MGJ_601
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
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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APC NAME: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
FORMULA: C11 H18 N5 O12 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)CP(O)(=O)OP(O)(O)=O)C(O)C3O
CMA NAME: N2-(CARBOXYETHYL)-L-ARGININE
FORMULA: C9 H18 N4 O4
SMILES: NC(=N)NCCCC(NCCC(O)=O)C(O)=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
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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