9QUG: UBC-Ubiquitin conjugate

Structure of a UBC-Ubiquitin conjugate. Determined by X-ray diffraction at 1.8 Å resolution. Released 21 Jan 2026.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,162
Mol. weight: 52.64 kDa
Ligands: P4K
Released: 21 Jan 2026

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

Secondary structure: helices and β-sheets

9QUG contains 20 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: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	929-932	4	4
α-helix	951-968	18
α-helix	969-970	2
β-strand	973-978	6	4
β-strand	984-990	7	4
α-helix	991-992	2
β-strand	1001-1007	7	4
α-helix	1016-1017	2
β-strand	1018-1021	4	4
β-strand	1030	1	5
β-strand	1033	1	5
β-strand	1039	1	5
β-strand	1041	1	3
α-helix	1042-1044	3
α-helix	1051-1053	3
α-helix	1061-1067	7
α-helix	1068-1072	5
α-helix	1077-1080	4
α-helix	1084-1086	3
α-helix	1091-1117	27
α-helix	1121-1123	3
α-helix	1124-1156	33
α-helix	1241-1243	3
α-helix	1259	1
α-helix	1261-1262	2
α-helix	1263-1282	20

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1
β-strand	75	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-B	C	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
(E3-independent) E2 ubiquitin-conjugating enzyme	A	protein	382	Homo sapiens	Q9C0C9 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9QUG_1 Polyubiquitin-B (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (A), FASTA

>9QUG_2 (E3-independent) E2 ubiquitin-conjugating enzyme (chains A)
MTFTSAKGEVFSVLEFAPSNHSFKKIEFQPPEAKKFFSTVRKEMALLATSLPEGIMVKTF
EDRMDLFSALIKGPTRTPYEDGLYLFDIQLPNIYPAVPPHFCYLSQCSGRLNPNLYDNGK
VKVSLLGTWIGKGTERWTSKSSLLQVLISIQGLILVNEPYYNEAGFDSDRGLQEGYENSR
CYNEMALIRVVQSMTQLVRRPPEVFEQEIRQHFSTGGWRLVNRIESWLETHALLEKAQAL
PNGVPKASSSPEPPAVAELSDSGQQEPEDGGPAPGEASQGSDSEGGAQGLASASRDHTDQ
TSETAPDASVPPSVKPKKRRKSYRSFLPEKSGYPDIGFPLFPLSKGFIKSIRGVLTQFRA
ALLEAGMPECTEDKGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
P4K	polyethylene glycol	C30 H62 O15	2

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

Primary citation

Structural basis for substrate recruitment and catalytic ubiquitin transfer by the E2/E3 hybrid enzyme UBE2O. Kordic, D., Williams, T.L., Deszcz, L. et al. J Biol Chem (2025) 302:111073-111073. DOI 10.1016/j.jbc.2025.111073 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Browse structure collections

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