Structure analysis with PISA¶
The PISA program analyses crystal structures to identify the component chemical monomers and the interfaces between the monomers including the monomers generated by applying symmetry to the input file coordinates. PISA will also evaluate the strength of interaction between the neighbouring monomers in a crystal and predict what would be the most stable multimer and therefore the most likely biological form of the structure.
Input¶
The input to the task is a PDB file containing the structure to be analysed.
Results¶
The report contains two main tables, the first describing the assemblies which were found, and the second describing the interfaces between the monomers in an assembly.
Assemblies table
This table gives information about the possible quaternery structures (“assemblies”) that PISA predicts. The table summarises the predicted assemblies.
The summary for each assembly consists of the following information:
mmSize is the number of macromolecular monomeric units in each assembly (consisting of protein and/or RNA/DNA, but not ligands), and the number of assemblies in the unit cell. For example: “2x6” indicates that the assembly contains 6 macromolecular monomeric units, and, for the given PQS set, a unit cell contains 2 assemblies of this type.
Formula and composition give respectively the chemical make up of the assembly. Note that the formula doesn’t use the chain ids from the entry, whereas the composition does.
ASA, BSA etc Details of solvent accessible and buried surface areas, and the solvation free energy on formation (ΔGint) and disassociation (ΔGdiss) of the assembly.
Notation for structures
Structures are indicated using the following notation.
Full chains without a chain ID are denoted {-}. Ligands are denoted:
[R]C:N
where R is the residue or ligand name, C is the chain, and N is the residue number. For example, [HEM]-:605 means protoporhyrin IX containing Fe (HEM) in chain without a chain ID, residue number 605.
Interfaces table
Interfaces between pairs of “structures” (i.e. chains and ligands) within the entry.
A results table shows details of each interface found, with one interface per row of the table:
Structure 1 is defined as a range of residues or as as a ligand name. {-} indicates the whole chain; other structures are the ligands and hetatm groups indicated as e.g. [GOL]-:1001.
Structure 2 is the second component which interfaces with the first. It is defined in a similar way to structure 1, however an additional symmetry operation is supplied (expressed either as a string or as a code).
For each structure the number of interfacing atoms (iNat) and residues (iNres) are indicated.
For each interface a number of quantities are listed:
Interface area (in A2)
ΔiG expressed in kcal/M, and an associated “P-value”. ΔiG is the solvation free energy gain on formation of the interface, with negative values indicating a hydrophobic interface.The P-value is a probability measure of the specificity of the interface:P=0.5 indicates that the ΔiG value is typical for this type of interface.
P>0.5 means that the interface is less hydrophobic than expected, suggesting that it is an artefact of crystal packing.
P<0.5 indicates interfaces with an unexpectedly large hydrophobicity, and thus a high specificity.
NHB, NSB The number of potential hydrogren bonds (NHB) and salt bridges (NSB) across the interface
CSS The “complexation significance score” CSS, which scores how significant the interface is for assembly formation.
A link (in the column labelled “x”) launches the selected viewer to visualise the interface. Clicking on the interface number (in the column marked “NN”) links to more detail about the interface in question.