7D3D: SPOP

Crystal structure of SPOP bound with a peptide. Determined by X-ray diffraction at 1.45 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,783
Mol. weight: 34.82 kDa
Released: 18 Nov 2020

Explore 7D3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D3D contains 14 α-helices and 26 β-strands across 4 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: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	93-96	4	1
β-strand	99	1	2

Chain A: 7 helices, 11 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	1	2
β-strand	60	1	3
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	113-119	7	1
β-strand	123-125	3	1
β-strand	130-138	9	2
α-helix	139-143	5
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-164	10	1
α-helix	165	1

Chain b: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	94-96	3	4
β-strand	97	1	3
β-strand	99	1	5

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	30-38	9	4
α-helix	41-43	3
β-strand	52-53	2	5
α-helix	54-56	3
β-strand	57-59	3	5
α-helix	61-63	3
β-strand	65-72	8	5
α-helix	78-80	3
β-strand	83-92	10	5
β-strand	98-107	10	4
β-strand	113-119	7	4
β-strand	123-125	3	4
β-strand	130-138	9	5
α-helix	139-143	5
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-165	11	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Speckle-type POZ protein	A, B	protein	139	Homo sapiens	O43791 (AlphaFold model)
Glu-val-ser-ile-ile-gln-gly-ala-asp-ser-thr-thr	a, b	protein	12	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>7D3D_1 Speckle-type POZ protein (chains A, B)
KVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLY
LLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEAN
GLLPDDKLTLFCEVSVVQD

Sequence of entity 2 (a, b), FASTA

>7D3D_2 GLU-VAL-SER-ILE-ILE-GLN-GLY-ALA-ASP-SER-THR-THR (chains a, b)
EVSIIQGADSTT

Primary citation

A peptide binder of E3 ligase adaptor SPOP disrupts oncogenic SPOP-protein interactions in kidney cancer cells. Wang, Z., Zhang, H., Chen, B. et al. Chin J Chem (2021) 39:271-280. DOI 10.1002/cjoc.202000462

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

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