6NYD: S. cerevisiae Ubc3

Crystal Structure of S. cerevisiae Ubc3 (Cdc34). Determined by X-ray diffraction at 1.65 Å resolution. Released 7 Aug 2019.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 1
Atoms: 1,515
Mol. weight: 22.87 kDa
Ligands: ZN
Released: 7 Aug 2019

Explore 6NYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NYD contains 7 α-helices and 7 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 C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-20	17
β-strand	29-34	6	1
β-strand	38-46	9	1
β-strand	60-65	6	1
β-strand	76-79	4	1
β-strand	88	1	2
β-strand	93	1	1
β-strand	94	1	2
α-helix	97-99	3
α-helix	121-133	13
α-helix	143-151	9
α-helix	153-167	15
α-helix	168-170	3
α-helix	172	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2-34 kDa	C	protein	197	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14682 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6NYD_1 Ubiquitin-conjugating enzyme E2-34 kDa (chains C)
GAMASRKSTASSLLLRQYRELTDPKKAIPSFHIELEDDSNIFTWNIGVMVLNEDSIYHGG
FFKAQMRFPEDFPFSPPQFRFTPAIYHPNVYRDGRLCISILHQSGDPMTDEPDAETWSPV
QTVESVLISIVSLLEDPNINSPANVDAAVDYRKNPEQYKQRVKMEVERSKQDIPKGFIMP
TSESAYISQSKLDEPES

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (ACT) are not listed.

Primary citation

Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Williams, K.M., Qie, S., Atkison, J.H. et al. Nat Commun (2019) 10:3296-3296. DOI 10.1038/s41467-019-11061-8 · PubMed

Other PDB entries of the same protein (UniProt P14682 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NYA 2.06 Å, Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin
6ZHU 3.18 Å, Yeast Uba1 in complex with Ubc3 and ATP
7K5J 3.42 Å, Structure of an E1-E2-ubiquitin thioester mimetic

Browse structure collections

About this viewer

MolViewer shows 6NYD 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.