9EWP: Ubiquitin-conjugating enzyme E2 6

Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain. Determined by X-ray diffraction at 1.21 Å resolution. Released 20 Nov 2024.

Method: X-ray diffraction
Resolution: 1.21 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 1,662
Mol. weight: 21.14 kDa
Ligands: CD
Released: 20 Nov 2024

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

Secondary structure: helices and β-sheets

9EWP contains 8 α-helices and 6 β-strands across 1 chain. 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-19	16
α-helix	21-22	2
β-strand	25-30	6	1
β-strand	33-42	10	1
α-helix	43-44	2
β-strand	53-59	7	1
α-helix	68-69	2
β-strand	70-73	4	1
β-strand	80	1	2
α-helix	104-116	13
β-strand	124	1	2
α-helix	129-145	17
α-helix	148-153	6
α-helix	155-172	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 6	A	protein	178	Saccharomyces cerevisiae	P33296 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EWP_1 Ubiquitin-conjugating enzyme E2 6 (chains A)
MATKQAHKRLTKEYKLMVENPPPYILARPNEDNILEWHYIITGPADTPYKGGQYHGTLTF
PSDYPYKPPAIRMITPNGRFKPNTRLCLSMSDYHPDTWNPGWSVSTILNGLLSFMTSDEA
TTGSITTSDHQKKTLARNSISYNTFQNVRFKLIFPEVVQENVETLEKRKLDELPETGG

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	4

Water and common crystallization additives (CL, NA, EDO) are not listed.

Primary citation

Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes. Swarnkar, A., Leidner, F., Rout, A.K. et al. EMBO J (2024) 43:6705-6739. DOI 10.1038/s44318-024-00301-3 · PubMed

Other PDB entries of the same protein (UniProt P33296 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EN5 1.33 Å, Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain
9EYH 2.6 Å, Ubiquitin conjugating enzyme Ubc6 UBC domain with isopeptide-linked ubiquitin

Browse structure collections

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