5IFR: Stable UBE2D3-UbDha conjugate

Structure of the stable UBE2D3-UbDha conjugate. Determined by X-ray diffraction at 2.2 Å resolution. Released 11 May 2016.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,854
Mol. weight: 25.67 kDa
Released: 11 May 2016

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

Secondary structure: helices and β-sheets

5IFR contains 11 α-helices and 17 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 A: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-2-15	18
α-helix	17-18	2
β-strand	21-25	5	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
β-strand	66-69	4	1
β-strand	75	1	2
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

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
α-helix	11	1
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	52	1	5
β-strand	54	1	5
β-strand	55	1	4
β-strand	66-71	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D3	A	protein	151	Homo sapiens	P61077 (AlphaFold model)
Polyubiquitin-B	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5IFR_1 Ubiquitin-conjugating enzyme E2 D3 (chains A)
GPLGSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHF
PTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPD
DPLVPEIARIYKTDRDKYNRISREWTQKYAM

Sequence of entity 2 (B), FASTA

>5IFR_2 Polyubiquitin-B (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGA

Primary citation

A cascading activity-based probe sequentially targets E1-E2-E3 ubiquitin enzymes. Mulder, M.P., Witting, K., Berlin, I. et al. Nat Chem Biol (2016) 12:523-530. DOI 10.1038/nchembio.2084 · PubMed

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

5EGG 1.76 Å, Crystal structure of human ubiquitin-conjugating enzyme UBCH5C
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
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

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