PatternQuery:Atlas

RNA

RNA kink-turn motif (Kt-7)

Example from 1ffk protein.

PQ expression

 Near(4, 
  RegularMotifs(’GGCGAAGAAC’, Type=’Nucleotide’), 
  RegularMotifs(’GGGAGCC’, Type=’Nucleotide’))

Some description goes here

Protein

C₂H₂ Zinc finger

Example from 4r2a protein.

PQ expression

RegularMotifs('.{2}C.{2,4}C.{12}H.{3,5}H').
	  ConnectedAtoms(1).
	  Filter(lambda m:
	    m.Find(Atoms('Zn').
              ConnectedResidues(1).
              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-X_2-4-C-X₁₂-H-X_3-5-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"))
  .ConnectedResidues(1)
  .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.