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Table 2 Structural families used as target queries to retrieve HTH-DNA structures. Indented rows indicate sub-fields, and multiple columns under “Setting” indicate a hierarchical choice

From: An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

Search field Setting
Structure features
 SCOP All α DNA/RNA-binding 3-helical bundle (core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down)
 SCOP All α lambda repressor-like DNA-binding domains
 SCOP All α Cyclin-like TFIIB
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.10
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.60
 CATH Mainly α Orthogonal Bundle 434 Repressor (Amino-terminal Domain) 1.10.260.40
 CATH α/β 2-Layer Sandwich CRO Repressor 3.30.240.10
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.400
 CATH Mainly α Orthogonal Bundle Factor For Inversion Stimulation; Chain: A 1.10.1680.10
 CATH Mainly α Orthogonal Bundle Chromosomal Replication Initiator Protein DnaA; Chain: A 1.10.1750.10
 CATH Mainly α Orthogonal Bundle Trp Operon Repressor; Chain A 1.10.1270.10
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.200
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.500
 CATH Mainly α Orthogonal Bundle Tetracycline Repressor; domain 2 1.10.357.10
 CATH Mainly α Orthogonal Bundle Putative cytoplasmic protein 1.10.3100.10
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.560
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.570
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.580
 CATH Mainly α Orthogonal Bundle Apoptosis Regulator Bcl-x 1.10.437.10
 CATH Mainly α Orthogonal Bundle Arc Repressor Mutant, subunit A 1.10.10.250
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