2H1K: Pdx1 homeodomain

Crystal structure of the Pdx1 homeodomain in complex with DNA. Determined by X-ray diffraction at 2.42 Å resolution. Released 20 Mar 2007.

Method: X-ray diffraction
Resolution: 2.42 Å
Organism: Mesocricetus auratus
Chains: 6
Atoms: 2,247
Mol. weight: 34.12 kDa
Released: 20 Mar 2007

Explore 2H1K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2H1K contains 7 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: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	28-38	11
α-helix	42-59	18

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	4-6	3
α-helix	10-22	13
α-helix	28-38	11
α-helix	42-57	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
15-mer DNA	C, E	DNA	15
15-mer DNA	D, F	DNA	15
Pancreatic and duodenal homeobox 1	A, B	protein	63	Mesocricetus auratus	P70118 (AlphaFold model)

Sequence of entity 1 (C, E), FASTA

>2H1K_1 15-mer DNA (chains C, E)
AGAAACTCATTAGAG

Sequence of entity 2 (D, F), FASTA

>2H1K_2 15-mer DNA (chains D, F)
TCTCTAATGAGTTTC

Sequence of entity 3 (A, B), FASTA

>2H1K_3 Pancreatic and duodenal homeobox 1 (chains A, B)
GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK
EED

Primary citation

Structural basis for induced fit mechanisms in DNA recognition by the pdx1 homeodomain. Longo, A., Guanga, G.P., Rose, R.B. Biochemistry (2007) 46:2948-2957. DOI 10.1021/bi060969l · PubMed

Other PDB entries of the same protein (UniProt P70118 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6F8G 2.03 Å, Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment

Browse structure collections

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