9HGG: SETD2 peptide

SETD2 peptide bound to SPOP MATH domain. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Apr 2025.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,329
Mol. weight: 18.18 kDa
Ligands: MG
Released: 23 Apr 2025

Explore 9HGG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HGG contains 6 α-helices and 11 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: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	1
α-helix	41-43	3
β-strand	52-53	2	2
α-helix	54-56	3
β-strand	57-58	2	2
β-strand	66-72	7	2
β-strand	83-92	10	2
β-strand	98-107	10	1
β-strand	113-118	6	1
β-strand	123-125	3	1
β-strand	130-138	9	2
α-helix	139-142	4
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-164	10	1
α-helix	165	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1373-1374	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Speckle-type POZ protein	A	protein	141	Homo sapiens	O43791 (AlphaFold model)
Histone-lysine N-methyltransferase SETD2	B	protein	17	Homo sapiens	Q9BYW2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9HGG_1 Speckle-type POZ protein (chains A)
AAKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLS
LYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDE
ANGLLPDDKLTLFCEVSVVQD

Sequence of entity 2 (B), FASTA

>9HGG_2 Histone-lysine N-methyltransferase SETD2 (chains B)
DKGSVQAPEISSNSIKD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5

Primary citation

Sequence rules for a long SPOP-binding degron required for protein ubiquitylation. Makhlouf, L., Mishra, M., Makhlouf, H. et al. Biochem J (2025) 482:583-600. DOI 10.1042/BCJ20253041 · PubMed

Other PDB entries of the same protein (UniProt O43791 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3IVV 1.25 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
7LIN 1.44 Å, X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide
7D3D 1.45 Å, Crystal structure of SPOP bound with a peptide
9HFV 1.45 Å, MyD88 peptide_2 bound to SPOP MATH domain
7LIP 1.48 Å, X-ray structure of SPOP MATH domain (D140G)
4HS2 1.53 Å, Crystal Structure of the Human SPOP C-terminal Domain
3HQL 1.66 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
3HQM 1.74 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
3IVB 1.75 Å, Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3…
6I5P 1.81 Å, Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment
6I68 1.85 Å, Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment
6I41 1.9 Å, Co-crystal structure of human SPOP MATH domain (wild-type) and human BRD3 fragment

Browse structure collections

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