9GLT: Yeast Ubc13 C87E

Crystal Structure of Yeast Ubc13 C87E. Determined by X-ray diffraction at 1.45 Å resolution. Released 7 May 2025.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 2,680
Mol. weight: 35.15 kDa
Released: 7 May 2025

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

Secondary structure: helices and β-sheets

9GLT contains 16 α-helices and 18 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 AAA: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	1
β-strand	34-40	7	1
α-helix	41-42	2
β-strand	50-57	8	1
α-helix	66-67	2
β-strand	68-71	4	1
β-strand	77	1	2
β-strand	80	1	2
β-strand	85	1	1
β-strand	86	1	2
α-helix	89-91	3
α-helix	101-113	13
α-helix	126-131	6
α-helix	133-147	15
β-strand	149-150	2	1

Chain BBB: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	3
β-strand	34-40	7	3
α-helix	41-42	2
β-strand	51-57	7	3
α-helix	66-67	2
β-strand	68-71	4	3
β-strand	77	1	4
β-strand	80	1	4
β-strand	85	1	3
β-strand	86	1	4
α-helix	89-91	3
α-helix	101-113	13
α-helix	126-131	6
α-helix	133-147	15
β-strand	149	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 13	AAA, BBB	protein	154	Saccharomyces cerevisiae	P52490 (AlphaFold model)

Sequence of entity 1 (AAA, BBB), FASTA

>9GLT_1 Ubiquitin-conjugating enzyme E2 13 (chains AAA, BBB)
GMASLPKRIIKETEKLVSDPVPGITAEPHDDNLRYFQVTIEGPEQSPYEDGIFELELYLP
DDYPMEAPKVRFLTKIYHPNIDRLGRIELDVLKTNWSPALQIRTVLLSIQALLASPNPND
PLANDVAEDWIKNEQGAKAKAREWTKLYAKKKPE

Primary citation

UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes. Kumar, M., Banerjee, S., Cohen-Kfir, E. et al. Nat Commun (2025) 16:3912-3912. DOI 10.1038/s41467-025-58826-y · PubMed

Other PDB entries of the same protein (UniProt P52490 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1JAT 1.6 Å, Mms2/Ubc13 Ubiquitin Conjugating Enzyme Complex
1JBB 2.0 Å, Ubiquitin Conjugating Enzyme, Ubc13
5OJW 2.0 Å, S. cerevisiae UBC13 - MMs2 complex
6ZHT 2.3 Å, Uba1-Ubc13 disulfide mediated complex
6ZHS 2.35 Å, Uba1 bound to two E2 (Ubc13) molecules
2GMI 2.5 Å, Mms2/Ubc13~Ubiquitin
4FH1 2.61 Å, S. cerevisiae Ubc13-N79A

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