RNA kink-turn motif (Kt-7)

Example from 1ffk protein.

PQ expression

  RegularMotifs(GGCGAAGAAC, Type=Nucleotide), 
  RegularMotifs(GGGAGCC, Type=Nucleotide))

Some description goes here


C2H2 Zinc finger

Example from 4r2a protein.

PQ expression

	  Filter(lambda m:
              Filter(lambda n: 
			(n.Count(Residues('Cys')) == 2) & (n.Count(Residues('His')) == 2))).
		SeqCount() > 0)

The classical C2H2 zinc finger domain is composed of a simple ββα fold, which is stabilized by a zinc ion coordinated by two histidine and two cysteine residues. The fold is often described by the pattern of X2-C-X2-4-C-X12-H-X3-5-H, where X stands for any amino acid, C is cysteine and H is histidine.

Rubredoxin binding site

Example from 1b13 protein.

PQ expression

Atoms("Fe").AmbientResidues(2.5).Filter(lambda l: l.Count(Residues("Cys")) == 4)

Rubredoxin active site contains an iron ion which is coordinated by the sulfurs of four conserved cysteine residues forming an almost regular tetrahedron. PQ expression identifies Fe atom coordinated by 4 cysteins.

PA-IIL lectin binding site

Example from 1gzt protein.

PQ expression

Near(4, Atoms("Ca"), Atoms("Ca"))
  .Filter(lambda l:
    l.Count(Or(Rings(5 * ["C"] + ["O"]), Rings(4 * ["C"] + ["O"]))) > 0)
  .Filter(lambda l: l.Count(Atoms("P")) == 0)

The PQ expression searches for 2 calcium ions at most 4Å apart, and all the residues with direct interaction with either of these ions. Furthermore, just the molecular patterns containing a residue with a furan or pyran ring were preserved. Additionally, nucleotides are filtered out as well.