3RKQ: NKX2.5 Homeodomain dimer

NKX2.5 Homeodomain dimer bound to ANF-242 DNA. Determined by X-ray diffraction at 1.7 Å resolution. Released 9 May 2012.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,942
Mol. weight: 25.93 kDa
Ligands: MG
Released: 9 May 2012

Explore 3RKQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RKQ contains 10 α-helices and 0 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	140-142	3
α-helix	144-146	3
α-helix	147-157	11
α-helix	165-175	11
α-helix	179-193	15

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	140-142	3
α-helix	144-146	3
α-helix	147-157	11
α-helix	165-175	11
α-helix	179-192	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Homeobox protein Nkx-2.5	A, B	protein	58	Homo sapiens	P52952 (AlphaFold model)
Anf-242 DNA	C	DNA	19
Anf-242 DNA	D	DNA	19

Sequence of entity 1 (A, B), FASTA

>3RKQ_1 Homeobox protein Nkx-2.5 (chains A, B)
GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK

Sequence of entity 2 (C), FASTA

>3RKQ_2 ANF-242 DNA (chains C)
TGAAGTGGGGGCCTCTTGA

Sequence of entity 3 (D), FASTA

>3RKQ_3 ANF-242 DNA (chains D)
TCAAGAGGCCCCCACTTCA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Crystal structure of the human NKX2.5 homeodomain in complex with DNA target. Pradhan, L., Genis, C., Scone, P. et al. Biochemistry (2012) 51:6312-6319. DOI 10.1021/bi300849c · PubMed

Other PDB entries of the same protein (UniProt P52952 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WC2 2.1 Å, Crystal Structure of a Ternary MEF2 Chimera/NKX2-5/myocardin enhancer DNA Complex
4S0H 2.82 Å, TBX5 DB, NKX2.5 HD, ANF DNA Complex
6WC5 2.9 Å, Crystal Structure of a Ternary MEF2B/NKX2-5/myocardin enhancer DNA Complex

Browse structure collections

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