3L1Y: Human UBC4 E2 conjugating enzyme

Name: PDB 3L1Y: Crystal structure of human UBC4 E2 conjugating enzyme
Published: 2010-05-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of human UBC4 E2 conjugating enzyme. Determined by X-ray diffraction at 1.6 Å resolution. Released 5 May 2010.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,449
Mol. weight: 18.05 kDa
Released: 5 May 2010

Explore 3L1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L1Y contains 7 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	21-25	5	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D2	A	protein	157	Homo sapiens	P62837 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3L1Y_1 Ubiquitin-conjugating enzyme E2 D2 (chains A)
MHHHHHHMNSMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVF
FLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLL
CDPNPDDPLVPEIARIYQTDREKYNRIAREWTQKYAM

Primary citation

Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4. Benirschke, R.C., Thompson, J.R., Nomine, Y. et al. Structure (2010) 18:955-965. DOI 10.1016/j.str.2010.04.017 · PubMed

Other PDB entries of the same protein (UniProt P62837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GLS 1.25 Å, Crystal Structure of Human UBCH5B C85E
2ESK 1.36 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
2ESQ 1.44 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
2ESO 1.5 Å, Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
2ESP 1.52 Å, Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
7AI0 1.56 Å, Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal…
5D1M 1.58 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A)
5D1L 1.62 Å, Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A)
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub
8GBQ 1.74 Å, Structure of RNF125 in complex with UbcH5b

Browse structure collections

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