9LHJ: UBE2N/UBE2V2

UBE2N/UBE2V2 complexed with a covalent inhibitor. Determined by X-ray diffraction at 1.68 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 1.68 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,260
Mol. weight: 68.13 kDa
Released: 14 May 2025

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

Secondary structure: helices and β-sheets

9LHJ contains 31 α-helices and 32 β-strands across 4 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-28	6	1
β-strand	31-40	10	1
α-helix	41-42	2
β-strand	51-57	7	1
α-helix	66-67	2
β-strand	68-71	4	1
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	124-131	8
α-helix	133-147	15

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-28	6	3
β-strand	31-40	10	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	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	124-131	8
α-helix	133-148	16

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	31-35	5	5
β-strand	45-51	7	5
α-helix	52-53	2
β-strand	62-68	7	5
α-helix	77-78	2
β-strand	79-82	4	5
β-strand	84	1	6
β-strand	91	1	7
β-strand	97	1	5
β-strand	98	1	7
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-125	11
α-helix	137	1
β-strand	142	1	6

Chain D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-24	14
β-strand	31-35	5	8
β-strand	45-51	7	8
α-helix	52-53	2
β-strand	62-68	7	8
α-helix	77-78	2
β-strand	79-82	4	8
β-strand	84	1	9
β-strand	91	1	10
β-strand	97	1	8
β-strand	98	1	10
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-125	11
α-helix	137	1
β-strand	142	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 N	A, B	protein	152	Homo sapiens	P61088 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 variant 2	C, D	protein	145	Homo sapiens	Q15819 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9LHJ_1 Ubiquitin-conjugating enzyme E2 N (chains A, B)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTXIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 2 (C, D), FASTA

>9LHJ_2 Ubiquitin-conjugating enzyme E2 variant 2 (chains C, D)
MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYEN
RIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQ
ELRRLMMSKENMKLPQPPEGQTYNN

Primary citation

Proteome-Wide Data Guides the Discovery of Lysine-Targeting Covalent Inhibitors Using DNA-Encoded Chemical Libraries. Wu, X., Li, S., Liang, T. et al. Angew Chem Int Ed Engl (2025) 64:e202505581-e202505581. DOI 10.1002/anie.202505581 · PubMed

Other PDB entries of the same protein (UniProt P61088 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ONL 1.35 Å, Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P
4ONM 1.35 Å, Crystal structure of human Mms2/Ubc13 - NSC697923
5YWR 1.47 Å, Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)
4ONN 1.5 Å, Crystal structure of human Mms2/Ubc13 - BAY 11-7082
9BIV 1.68 Å, Crystal Structure of Ubc13 with a New Active Site Loop Conformation
4DHI 1.8 Å, Structure of C. elegans OTUB1 bound to human UBC13
4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
4NRG 1.95 Å, Crystal Structure of a human Mms2/Ubc13 D118G mutant
6ULH 1.97 Å, Structure of MavC in complex with its substrate in R3 spacegroup
4TKP 2.08 Å, Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor
6P5B 2.1 Å, Crystal Structure of MavC in Complex with Ub-UbE2N

Browse structure collections

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