3PTF: Ubiquitin-conjugating enzyme E2 D1

X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin. Determined by X-ray diffraction at 2.7 Å resolution. Released 11 May 2011.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Homo sapiens, Homo Sapiens
Chains: 4
Atoms: 3,648
Mol. weight: 52.27 kDa
Released: 11 May 2011

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

Secondary structure: helices and β-sheets

3PTF contains 18 α-helices and 29 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-4-15	20
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	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 B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-3-15	19
β-strand	21-25	5	3
β-strand	32-38	7	3
α-helix	39-40	2
β-strand	49-55	7	3
β-strand	66-69	4	3
β-strand	75	1	4
β-strand	78	1	4
β-strand	83	1	3
β-strand	84	1	4
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	7
β-strand	12-17	6	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
β-strand	55	1	8
β-strand	66-71	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D1	A, B	protein	153	Homo sapiens	P51668 (AlphaFold model)
Polyubiquitin-B	C, D	protein	79	Homo Sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3PTF_1 Ubiquitin-conjugating enzyme E2 D1 (chains A, B)
GSHMLEMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTV
HFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPN
PDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM

Sequence of entity 2 (C, D), FASTA

>3PTF_2 Polyubiquitin-B (chains C, D)
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRGG

Primary citation

Modulation of K11-Linkage Formation by Variable Loop Residues within UbcH5A. Bosanac, I., Phu, L., Pan, B. et al. J Mol Biol (2011) 408:420-431. DOI 10.1016/j.jmb.2011.03.011 · 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
6D4P 2.11 Å, Ube2D1 in complex with ubiquitin variant Ubv.D1.1
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
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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