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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