2C4P: Human ubiquitin-conjugating enzyme UbcH5A

Crystal structure of human ubiquitin-conjugating enzyme UbcH5A. Determined by X-ray diffraction at 2.35 Å resolution. Released 22 Nov 2006.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,458
Mol. weight: 37.39 kDa
Released: 22 Nov 2006

Explore 2C4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2C4P contains 11 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
β-strand	21-26	6	1
β-strand	29-38	10	1
β-strand	49-55	7	1
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	0-11	12
β-strand	23-25	3	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	87-90	4
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 D1	A, B	protein	165	HOMO SAPIENS	P51668 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2C4P_1 UBIQUITIN-CONJUGATING ENZYME E2 D1 (chains A, B)
MKHHHHHHPMSGLVPRGSMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPD
SAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKV
LLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM

Primary citation

Structures of Two Human Ubiquitin-Conjugating Enzymes from Twinned Crystals. Dodd, R.B., Read, R.J. To be published.

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
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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