6D4P: Ube2D1

Ube2D1 in complex with ubiquitin variant Ubv.D1.1. Determined by X-ray diffraction at 2.11 Å resolution. Released 17 Jul 2019.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,757
Mol. weight: 26.73 kDa
Released: 17 Jul 2019

Explore 6D4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D4P contains 10 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-15	16
β-strand	22-25	4	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
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

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	3
β-strand	12-17	6	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D1	A	protein	149	Homo sapiens	P51668 (AlphaFold model)
Ubiquitin Variant Ubv.D1.1	C	protein	88	Homo sapiens	Q59EM9

Sequence of entity 1 (A), FASTA

>6D4P_1 Ubiquitin-conjugating enzyme E2 D1 (chains A)
GAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPT
DYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDP
LVPDIAQIYKSDKEKYNRHAREWTQKYAM

Sequence of entity 2 (C), FASTA

>6D4P_2 Ubiquitin Variant Ubv.D1.1 (chains C)
GAGGDYKDDDDKMQIFVKKFWGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK
QLEDGRTLSDYNIQKKFTLYLAYGLRAG

Primary citation

Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes. Garg, P., Ceccarelli, D.F., Keszei, A.F.A. et al. J Mol Biol (2020) 432:952-966. DOI 10.1016/j.jmb.2019.09.024 · PubMed

Other PDB entries of the same protein (UniProt P51668 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QPL 1.9 Å, Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex
2YHO 2.1 Å, The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor
4AP4 2.21 Å, Rnf4 - ubch5a - ubiquitin heterotrimeric complex
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
2C4P 2.35 Å, Crystal structure of human ubiquitin-conjugating enzyme UbcH5A
7ZJ3 2.53 Å, Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate
5TUT 2.6 Å, UbcH5a-Ub isopeptide conjugate
3PTF 2.7 Å, X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin
9V09 3.25 Å, Cryo-EM structure of lenalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
9V0C 3.27 Å, Cryo-EM structure of iberdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
3OJ4 3.4 Å, Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex
9UUM 3.41 Å, Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…

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