5TUT: UbcH5a-Ub isopeptide conjugate

UbcH5a-Ub isopeptide conjugate. Determined by X-ray diffraction at 2.6 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,793
Mol. weight: 25.51 kDa
Released: 8 Nov 2017

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

Secondary structure: helices and β-sheets

5TUT contains 11 α-helices and 14 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-1-15	17
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	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-141	11
α-helix	142-146	5

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	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	150	Homo sapiens	P51668 (AlphaFold model)
Ubiquitin	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5TUT_1 Ubiquitin-conjugating enzyme E2 D1 (chains A)
GSHMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFP
TDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPDD
PLVPDIAQIYKSDKEKYNRHAREWTQKYAM

Sequence of entity 2 (B), FASTA

>5TUT_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

UbcH5a-Ub isopeptide conjugate. Sanchez, J.G., Wagner, J.M., Pornillos, O. 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
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
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…

Browse structure collections

About this viewer

MolViewer shows 5TUT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.