3K9P: E2-25K and ubiquitin complex

The crystal structure of E2-25K and ubiquitin complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 8 Sept 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,137
Mol. weight: 32.95 kDa
Released: 8 Sept 2010

Explore 3K9P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3K9P contains 13 α-helices and 15 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	20-23	4
β-strand	27-31	5	1
β-strand	38-44	7	1
α-helix	45-46	2
β-strand	55-61	7	1
α-helix	70-71	2
β-strand	72-75	4	1
β-strand	81	1	2
β-strand	84	1	2
β-strand	90	1	1
β-strand	91	1	2
α-helix	94-96	3
α-helix	106-118	13
α-helix	128-136	9
α-helix	138-153	16
α-helix	160-170	11
α-helix	176-185	10
α-helix	190-196	7

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-44	2	3
β-strand	49	1	3
β-strand	55	1	4
β-strand	66-69	4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 K	A	protein	217	Homo sapiens	P61086 (AlphaFold model)
Ubiquitin	B	protein	79	Homo sapiens	P62979 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3K9P_1 Ubiquitin-conjugating enzyme E2 K (chains A)
GSHMASMTGGQQMGRGSMANIAVQRIKREFKEVLKSEETSKNQIKVDLVDENFTELRGEI
AGPPDTPYEGGRYQLEIKIPETYPFNPPKVRFITKIWHPNISSVTGAICLDILKDQWAAA
MTLRTVLLSLQALLAAAEPDDPQDAVVANQYKQNPEMFKQTARLWAHVYAGAPVSSPEYT
KKIENLCAMGFDRNAVIVALSSKSWDVETATELLLSN

Sequence of entity 2 (B), FASTA

>3K9P_2 Ubiquitin (chains B)
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRGG

Primary citation

Structural basis of E2-25K/UBB+1 interaction leading to proteasome inhibition and neurotoxicity. Ko, S., Kang, G.B., Song, S.M. et al. J Biol Chem (2010) 285:36070-36080. DOI 10.1074/jbc.M110.145219 · PubMed

Other PDB entries of the same protein (UniProt P61086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3K9O 1.8 Å, The crystal structure of E2-25K and UBB+1 complex
3E46 1.86 Å, Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington interacting…
5DFL 2.1 Å, Crystal structure of Ube2K~Ubiquitin conjugate
6JB7 2.1 Å, Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A…
3F92 2.23 Å, Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington Interacting…
7MYH 2.39 Å, Ubiquitin variant UbV.k.2 in complex with Ube2k
1YLA 2.4 Å, Ubiquitin-conjugating enzyme E2-25 kDa (Huntington interacting protein 2)
7OJX 2.4 Å, E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for…
6IF1 2.47 Å, Crystal structure of Ube2K and K48-linked di-ubiquitin complex
2O25 2.6 Å, Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9
6JB6 2.7 Å, Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A…
7MYF 3.0 Å, Ubiquitin variant UbV.k.1 in complex with Ube2k

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