5EGG: Human ubiquitin-conjugating enzyme UBCH5C

Crystal structure of human ubiquitin-conjugating enzyme UBCH5C. Determined by X-ray diffraction at 1.76 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,245
Mol. weight: 17.78 kDa
Released: 2 Nov 2016

Explore 5EGG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EGG 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 A: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	22-25	4	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D3	A	protein	156	Homo sapiens	P61077 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5EGG_1 Ubiquitin-conjugating enzyme E2 D3 (chains A)
MGHHHHHHGMALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFF
LTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLC
DPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM

Primary citation

Structural analysis of recombinant human ubiquitin-conjugating enzyme UbcH5c. Wu, F., Zhu, J., Li, H. et al. Acta Pharm Sin B (2017) 7:390-394. DOI 10.1016/j.apsb.2016.12.008 · PubMed

Other PDB entries of the same protein (UniProt P61077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1X23 1.85 Å, Crystal structure of ubch5c
4S3O 2.0 Å, PCGF5-RING1B-UbcH5c complex
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
5IFR 2.2 Å, Structure of the stable UBE2D3-UbDha conjugate
8UQ9 2.3 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker
8UQ8 2.34 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
3UGB 2.35 Å, UbcH5c~Ubiquitin Conjugate
8AMS 2.4 Å, Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin
8UQB 2.48 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
6T7F 2.58 Å, RCR E3 ligase E2-Ubiquitin transthiolation intermediate
8UQC 2.61 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
3RPG 2.65 Å, Bmi1/Ring1b-UbcH5c complex structure

Browse structure collections

About this viewer

MolViewer shows 5EGG 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.