5LBN: UBC core domain of UBE2E1/UbcH6

High-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6. Determined by X-ray diffraction at 1.42 Å resolution. Released 14 Feb 2018.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,505
Mol. weight: 17.8 kDa
Released: 14 Feb 2018

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

Secondary structure: helices and β-sheets

5LBN contains 9 α-helices and 8 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
α-helix	47-61	15
α-helix	63-64	2
β-strand	67-71	5	1
β-strand	78-84	7	1
α-helix	85-86	2
β-strand	95-101	7	1
α-helix	110-111	2
β-strand	112-115	4	1
β-strand	121	1	2
β-strand	124	1	2
β-strand	129	1	1
β-strand	130	1	2
α-helix	133-135	3
α-helix	145-157	13
α-helix	167-175	9
α-helix	177-191	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 E1	A	protein	158	Homo sapiens	P51965 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5LBN_1 Ubiquitin-conjugating enzyme E2 E1 (chains A)
GSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGV
FFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSL
LTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT

Primary citation

Structure of a TRIM21 - UBE2E1 complex reveals the specificity of E2 and ubiquitin recognition by TRIM E3 RINGs. Anandapadamanaban, M., Moche, M., Sunnerhagen, M. To be published.

Other PDB entries of the same protein (UniProt P51965 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BZH 1.6 Å, Crystal structure of human ubiquitin-conjugating enzyme E2 E1
1XR9 1.79 Å, Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and…
4JJQ 1.95 Å, Crystal structure of usp7-ntd with an e2 enzyme
8IYA 2.43 Å, Complex of SETDB1-derived peptide bound to UBE2E1
6FGA 2.82 Å, Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2…

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