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

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

(click anywhere in this window to remove it)
1q19
BIOSYNTHETIC PROTEIN HEADER
CARBAPENAM SYNTHETASE TITLE
CARA 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
APC N 505
244M PRO
245M LEU
246M SER
248M GLY
249M LEU
250M ASP
251M SER
268M TYR
269M SER
270M ILE
277M GLU
326M GLY
327M LEU
330M VAL
343M THR
344M GLY
345M TYR
348M ASP
421M LYS
425M ARG
441M ARG
442M LYS
443M LYS
444M ILE
445M GLY
446M ILE
450M SER
APC F 505
244E PRO
245E LEU
246E SER
248E GLY
249E LEU
250E ASP
251E SER
268E TYR
269E SER
270E ILE
277E GLU
323E ILE
326E GLY
327E LEU
330E VAL
343E THR
344E GLY
345E TYR
348E ASP
421E LYS
441E ARG
442E LYS
443E LYS
444E ILE
445E GLY
446E ILE
450E SER
APC J 505
244I PRO
245I LEU
246I SER
248I GLY
249I LEU
250I ASP
251I SER
268I TYR
269I SER
270I ILE
277I GLU
278I PHE
327I LEU
330I VAL
343I THR
344I GLY
345I TYR
348I ASP
421I LYS
441I ARG
442I LYS
443I LYS
444I ILE
445I GLY
446I ILE
450I SER
APC B 505
244A PRO
245A LEU
246A SER
248A GLY
249A LEU
250A ASP
251A SER
268A TYR
269A SER
270A ILE
277A GLU
278A PHE
327A LEU
330A VAL
343A THR
344A GLY
345A TYR
348A ASP
421A LYS
441A ARG
442A LYS
443A LYS
444A ILE
445A GLY
446A ILE
450A SER
MG O 504
246M SER
248M GLY
277M GLU
444M ILE
445M GLY
MG G 504
246E SER
248E GLY
277E GLU
444E ILE
445E GLY
446E ILE
MG K 504
246I SER
248I GLY
277I GLU
441I ARG
444I ILE
445I GLY
MG C 504
246A SER
248A GLY
277A GLU
441A ARG
444A ILE
445A GLY
SSC P 506
319M LEU
320M SER
323M ILE
344M GLY
345M TYR
346M GLY
348M ASP
349M LEU
354M ILE
371M GLN
374M ARG
375M THR
380M GLU
445M GLY
446M ILE
447M HIS
SSC H 506
319E LEU
323E ILE
344E GLY
345E TYR
346E GLY
347E SER
348E ASP
349E LEU
354E ILE
371E GLN
374E ARG
375E THR
380E GLU
447E HIS
SSC L 506
319I LEU
323I ILE
344I GLY
345I TYR
346I GLY
348I ASP
349I LEU
354I ILE
371I GLN
380I GLU
443I LYS
445I GLY
446I ILE
447I HIS
SSC D 506
319A LEU
320A SER
323A ILE
344A GLY
345A TYR
346A GLY
347A SER
348A ASP
349A LEU
354A ILE
371A GLN
374A ARG
375A THR
380A GLU
443A LYS
446A ILE
447A HIS
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.

(click anywhere in this window to remove it)

Links to external databases:

LigPlot (hosted at the EBI):

» Jmol
» Jmol
» Jmol
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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
1q15 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.

(click anywhere in this window to remove it)
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
SSC NAME: (2S,5S)-5-CARBOXYMETHYLPROLINE
FORMULA: C7 H11 N1 O4
SMILES: OC(=O)CC1CCC(N1)C(O)=O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
v9.1
October 2010
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
Script execution time: 0.132 seconds