7MYF: Ubiquitin variant UbV.k.1

Ubiquitin variant UbV.k.1 in complex with Ube2k. Determined by X-ray diffraction at 3.0 Å resolution. Released 25 Aug 2021.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,707
Mol. weight: 41.81 kDa
Released: 25 Aug 2021

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

Secondary structure: helices and β-sheets

7MYF contains 14 α-helices and 21 β-strands across 3 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-23	17
β-strand	28-31	4	1
β-strand	38-44	7	1
α-helix	45-46	2
β-strand	55-61	7	1
β-strand	72-75	4	1
β-strand	81	1	2
β-strand	84	1	2
β-strand	91	1	2
α-helix	94-97	4
α-helix	106-118	13
α-helix	128-136	9
α-helix	138-152	15
α-helix	160-170	11
α-helix	176-185	10
α-helix	190-193	4

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	12-17	6	1
β-strand	22	1	3
α-helix	23-33	11
β-strand	42-44	3	1
α-helix	48	1
β-strand	49	1	1
α-helix	50-51	2
β-strand	55	1	3
β-strand	65-70	6	1

Chain C: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-33	11
β-strand	42-45	4	4
β-strand	48-49	2	4
β-strand	55	1	5
α-helix	58-60	3
β-strand	66-70	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 K	A	protein	201	Homo sapiens	P61086 (AlphaFold model)
Ubiquitin variant UbV.k.1	B	protein	94	Homo sapiens	P0CG47 (AlphaFold model)
Ubiquitin	C	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7MYF_1 Ubiquitin-conjugating enzyme E2 K (chains A)
MAANIAVQRIKREFKEVLKSEETSKNQIKVDLVDENFTELRGEIAGPPDTPYEGGRYQLE
IKIPETYPFNPPKVRFITKIWHPNISSVTGAIKLDILRDQWAAAMTLRTVLLSLQALLAA
AEPDDPQDAVVANQYKQNPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLCAMGFDRNAV
IVALSSKSWDVETATELLLSN

Sequence of entity 2 (B), FASTA

>7MYF_2 Ubiquitin variant UbV.k.1 (chains B)
GPGDYKDDDDKMFIFVKTLTRKYITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFSGQQ
LEDGRTLSDYNIQEFSFLHLISRLRGVYQGGSGG

Sequence of entity 3 (C), FASTA

>7MYF_3 Ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Identification of Ubiquitin Variants That Inhibit the E2 Ubiquitin Conjugating Enzyme, Ube2k. Middleton, A.J., Teyra, J., Zhu, J. et al. ACS Chem Biol (2021) 16:1745-1756. DOI 10.1021/acschembio.1c00445 · PubMed

Other PDB entries of the same protein (UniProt P61086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3K9O 1.8 Å, The crystal structure of E2-25K and UBB+1 complex
3E46 1.86 Å, Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington interacting…
5DFL 2.1 Å, Crystal structure of Ube2K~Ubiquitin conjugate
6JB7 2.1 Å, Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A…
3F92 2.23 Å, Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington Interacting…
7MYH 2.39 Å, Ubiquitin variant UbV.k.2 in complex with Ube2k
1YLA 2.4 Å, Ubiquitin-conjugating enzyme E2-25 kDa (Huntington interacting protein 2)
7OJX 2.4 Å, E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for…
6IF1 2.47 Å, Crystal structure of Ube2K and K48-linked di-ubiquitin complex
2O25 2.6 Å, Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9
6JB6 2.7 Å, Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A…
3K9P 2.8 Å, The crystal structure of E2-25K and ubiquitin complex

Browse structure collections

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