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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3iiq
HYDROLASE HEADER
CRYSTALLOGRAPHIC ANALYSIS OF BACTERIAL SIGNAL PEPTIDASE IN TERNARY COMPLEX WITH ARYLOMYCIN A2 AND A BETA-SULTAM INHIBITOR TITLE
SIGNAL PEPTIDASE I 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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ARY A 401
79A PHE
81A TYR
82A GLU
83A PRO
84A PHE
85A GLN
86A ILE
87A PRO
88A SER
90A SER
100A PHE
132A VAL
141A LEU
142A ASP
143A TYR
144A ILE
145A LYS
300A TRP
ARY B 402
81B TYR
82B GLU
83B PRO
84B PHE
85B GLN
86B ILE
87B PRO
88B SER
90B SER
100B PHE
132B VAL
141B LEU
142B ASP
143B TYR
144B ILE
145B LYS
300B TRP
JZA B 1
87B PRO
88B SER
89B GLY
90B SER
143B TYR
145B LYS
277B ASN
278B SER
279B ALA
307B GLU
JZA A 1
87A PRO
88A SER
89A GLY
90A SER
143A TYR
145A LYS
208A PHE
277A ASN
278A SER
279A ALA
307A GLU
CCN A 326
93A PRO
94A THR
299A ILE
318A ARG
321A GLY
322A ILE
323A HIS
GOL A 2
93A PRO
236A ARG
318A ARG
321A GLY
CCN A 327
94A THR
235A HIS
236A ARG
323A HIS
GOL A 3
183B THR
184B TYR
185B SER
186B ASN
226B ARG
321A GLY
322A ILE
323A HIS
TRT B 324
194B GLN
196B PHE
206B SER
240B VAL
242B ILE
243B ALA
249B MET
275B ARG
276B ASP
277B ASN
278B SER
279B ALA
283B TYR
GOL A 4
299A ILE
317A SER
318A ARG
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
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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).

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apo-structure
pdb ID
1kn9 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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CCN NAME: ACETONITRILE
FORMULA: C2 H3 N1
SMILES: CC#N
GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
ARY NAME: ARYLOMYCIN A2
FORMULA: C42 H60 N6 O11
SMILES: CC(C)CCCCCCCCC(=O)N(C)C(CO)C(=O)NC(C)C(=O)NCC(=O)N(C)C1C(=O)NC(C)C(=O)NC(Cc2ccc(O)c(c2)c3cc1ccc3O)C(O)=O
TRT NAME: FRAGMENT OF TRITON X-100
FORMULA: C21 H36 O4
SMILES: COCCOCCOCCOc1ccc(cc1)C(C)(C)CC(C)(C)C
JZA NAME: not_found
FORMULA: not_found
SMILES: not_found
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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