9HFV: MyD88 peptide_2

MyD88 peptide_2 bound to SPOP MATH domain. Determined by X-ray diffraction at 1.45 Å resolution. Released 18 Jun 2025.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,376
Mol. weight: 18.32 kDa
Released: 18 Jun 2025

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

Secondary structure: helices and β-sheets

9HFV 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	28-38	11	1
α-helix	41-43	3
β-strand	52-53	2	2
α-helix	54-56	3
β-strand	57	1	2
β-strand	66-72	7	2
α-helix	78-80	3
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	155-165	11	1

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Speckle-type POZ protein	A	protein	141	Homo sapiens	O43791 (AlphaFold model)
Myeloid differentiation primary response protein MyD88	B	protein	20	Homo sapiens	Q99836 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9HFV_1 Speckle-type POZ protein (chains A)
APKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLS
LYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDE
ANGLLPDDKLTLFCEVSVVQD

Sequence of entity 2 (B), FASTA

>9HFV_2 Myeloid differentiation primary response protein MyD88 (chains B)
KPLQVAAVDSSVPRTAELAG

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
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
9HGG 1.9 Å, SETD2 peptide bound to SPOP MATH domain

Browse structure collections

About this viewer

MolViewer shows 9HFV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.