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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3a2u
MEMBRANE PROTEIN HEADER
CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEIN PORB FROM NEISSE MENINGITIDIS IN COMPLEX WITH AMP-PNP TITLE
OUTER MEMBRANE PROTEIN II 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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ANP D 342
9C LYS
39C PHE
40C GLY
42C LYS
60C GLN
62C GLU
64C LYS
77C ARG
78C GLN
96C ASN
100C LYS
101C ASP
104C ASP
107C ASN
110C GLU
116C GLU
125C GLY
128C GLU
130C ARG
202C GLU
340C LYS
ANP F 342
9E LYS
39E PHE
40E GLY
42E LYS
60E GLN
62E GLU
64E LYS
77E ARG
78E GLN
96E ASN
100E LYS
101E ASP
104E ASP
107E ASN
110E GLU
116E GLU
125E GLY
128E GLU
130E ARG
202E GLU
340E LYS
ANP B 342
9A LYS
39A PHE
40A GLY
42A LYS
60A GLN
62A GLU
64A LYS
77A ARG
78A GLN
96A ASN
100A LYS
101A ASP
104A ASP
107A ASN
110A GLU
116A GLU
125A GLY
128A GLU
130A ARG
202A GLU
340A 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).

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

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apo-structure
pdb ID
3a2r Details
other holo-structures
pdb ID Ligand Unique ID
3a2s SUCB_342 Details
SUCH_342
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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ANP NAME: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
FORMULA: C10 H17 N6 O12 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)NP(O)(O)=O)C(O)C3O
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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