Ligbase HELP

LigBase Help Page

LigBase is powered by a MySQL Relational Database. The contents may be searched by entering an identifier in one or both of the textfields. Search terms include the PDB Code (1fus), Ligand Code (ATP), PDB description - words that can be found in the PDB HEADER,the number of atoms found in a ligand, the date (ie 21-JAN-98), the experimental method (X-RAY or NMR). The And/Or button can be used to combine search terms or to look for two terms at the same time. Covalent, Noncovalent or BOTH types of Ligands can be selected. LigBase considers ligands closer than 1.80 Angstroms to any protein atom to be a covalently bound ligand. The number of results to be displayed is controlled by the button at the lower left.

The results of the search are displayed in a table containing information about the ligands identified and the PDB structures in which they are found.

PDB designated Ligand code.

Lig Description

PDB designated description, usually taken from the PDB file.

The number of atoms in the ligand.

The chains which have proteins atoms closer than 5 Angstroms to the ligand.

The PDB designated Ligand identification number. This number is not always unique in a pdb file because the same ligand in a different chain may have the same identification number.

Designates whether the ligand is NCO (not covalent) or COV (covalent or at least the ligand is closer than 1.8 Angstroms to a protein atom.)

The date is the deposition date with the Protein Data Bank.

The PDB code provides a link to the PDB for this protein.

The M column provides a link to all models that were made using the PDB structure as a template.

The C column provides a link to the CATH database for this protein.

The LP column provides a two dimensional diagram of the ligand and the surrounding protein residues (Wallace AC, Laskowski RA & Thornton JM (1995) LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Prot. Eng., 8, 127-134.)

Protein description

Taken from the PDB Header.

Experimental procedure for structure determination, always NMR or X-Ray, no model structures are taken from the PDB.

The X-RAY resolution for the structure or the number of models in the ensemble for NMR structures.

Provides a link to other structures that are similar to the selected chain using the CE database. Similar structures may bind to the same or similar ligands.

Alignments in LigBase are currently based on pairwise alignments generated by the Combinatorial Extension Program CE - http://cl.sdsc.edu/ce/ce_help.html (Ilya N. Shindyalov and Philip E. Bourne (1998) Protein Engineering 11(9) 739-747.) Initially, the CE database is screened to identify the structural family of the ligand binding chain. Members of the family include both representatives and similiar chains.

As outlined on the CE pages, the criteria for a representative is that -

- The RMSD between two chains is less than 2A.

- The length difference between two chains is less than 10%.

- The number of gap postions in alignment between two chains is less than 20% of aligned residue positions.

- At least 2/3 of residue postions in represented chain are aligned with representing chain.

the criteria for a similar chain is that -

- The Z-score if greater than 3.8. The Z-score is a measure of structural similarity compared to random alignments.

- The chain does not meet all the requirements to be a representative.

Restricting structural alignments

The user may restrict the alignments in CE database according to several criteria -

- Sequence Identity % of residues that are identical for an alignment

- Alignment Length number of residues that are aligned

- RMSD Root Mean Square deviation of the aligned structures

- Z-score measure of the structural similarity, # of Standard deviations better than a random alignment

- Gap Length number residues that are not aligned within the alignment

- Ligand Bound flag to select chains with an identical ligand bound

Selecting structural alignments

Chains which match the search criteria are displayed with a check box next to the them.

Select the chains of interest to compare active residues in the alignment and/or to compare their structures.

Alignment Results

Protein residues within 5 Angstroms of the ligand selected are displayed in Red in the first table. If

multiple chains are involved, the contact residues for subsequent chains are shown below.

The Results of the pairwise CE alignments are shown next for each chain selected.

LigBase builds and displays multiple alignments from the series of pairwise alignments for the selected chain.

Residues which are within 5 Angstroms of the ligand are shown in Red.

Residues from other chains which align with the contact residues for the ligand are shown in Orange.

Conservation of contact residues may indicate a binding site for a similar ligand.

The ModView Structure/Alignment Graphics Viewer

Obtain the 2 ModView plugin files

(http://guitar.compbio.ucsf.edu/modview)

and put both files in your home/.netscape/plugins directory

Choose ModView as your application for pdb files and alignment files under the Netscape windows preferences

Push the Run ModView button on the alignment page to view structures and alignments together.