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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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.

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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 E 403
244C PRO
245C LEU
246C SER
248C GLY
249C LEU
250C ASP
251C SER
268C TYR
269C SER
270C ILE
277C GLU
326C GLY
327C LEU
330C VAL
343C THR
344C GLY
345C TYR
348C ASP
421C LYS
425C ARG
441C ARG
442C LYS
443C LYS
444C ILE
445C GLY
446C ILE
450C SER
APC E 402
244B PRO
245B LEU
246B SER
248B GLY
249B LEU
250B ASP
251B SER
268B TYR
269B SER
270B ILE
277B GLU
278B PHE
327B LEU
330B VAL
343B THR
344B GLY
345B TYR
348B ASP
421B LYS
441B ARG
442B LYS
443B LYS
444B ILE
445B GLY
446B ILE
450B SER
APC E 404
244D PRO
245D LEU
246D SER
248D GLY
249D LEU
250D ASP
251D SER
268D TYR
269D SER
270D ILE
277D GLU
323D ILE
326D GLY
327D LEU
330D VAL
343D THR
344D GLY
345D TYR
348D ASP
421D LYS
441D ARG
442D LYS
443D LYS
444D ILE
445D GLY
446D ILE
450D SER
APC E 401
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 E 412
246C SER
248C GLY
277C GLU
444C ILE
445C GLY
MG E 411
246B SER
248B GLY
277B GLU
441B ARG
444B ILE
445B GLY
MG E 410
246D SER
248D GLY
277D GLU
444D ILE
445D GLY
446D ILE
MG E 409
246A SER
248A GLY
277A GLU
441A ARG
444A ILE
445A GLY
SSC E 408
319C LEU
320C SER
323C ILE
344C GLY
345C TYR
346C GLY
348C ASP
349C LEU
354C ILE
371C GLN
374C ARG
375C THR
380C GLU
445C GLY
446C ILE
447C HIS
SSC E 406
319B LEU
323B ILE
344B GLY
345B TYR
346B GLY
348B ASP
349B LEU
354B ILE
371B GLN
380B GLU
443B LYS
445B GLY
446B ILE
447B HIS
SSC E 407
319D LEU
323D ILE
344D GLY
345D TYR
346D GLY
347D SER
348D ASP
349D LEU
354D ILE
371D GLN
374D ARG
375D THR
380D GLU
447D HIS
SSC E 405
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.

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Links to external databases:

LigPlot (hosted at the EBI):

» Jmol
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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).

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

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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.

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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
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++]
v4.0
May 2008
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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