5DFL: Ube2K~Ubiquitin conjugate

Crystal structure of Ube2K~Ubiquitin conjugate. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Dec 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,247
Mol. weight: 31.26 kDa
Released: 2 Dec 2015

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

Secondary structure: helices and β-sheets

5DFL contains 15 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	20-23	4
β-strand	27-31	5	3
β-strand	38-44	7	3
α-helix	45-46	2
β-strand	55-61	7	3
α-helix	70-71	2
β-strand	72-75	4	3
β-strand	81	1	4
β-strand	84	1	4
β-strand	90	1	3
β-strand	91	1	4
α-helix	94-96	3
α-helix	106-118	13
α-helix	128-136	9
α-helix	138-153	16
α-helix	160-171	12
α-helix	176-185	10
α-helix	190-198	9

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 K	A	protein	200	Homo sapiens	P61086 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5DFL_1 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (A), FASTA

>5DFL_2 Ubiquitin-conjugating enzyme E2 K (chains A)
AANIAVQRIKREFKEVLKSEETSKNQIKVDLVDENFTELRGEIAGPPDTPYEGGRYQLEI
KIPETYPFNPPKVRFITKIWHPNISSVTGAIKLDILRDQWAAAMTLRTVLLSLQALLAAA
EPDDPQDAVVANQYKQNPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLSAMGFDRNAVI
VALSSKSWDVETATELLLSN

Primary citation

The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K. Middleton, A.J., Day, C.L. Sci Rep (2015) 5:16793-16793. DOI 10.1038/srep16793 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Browse structure collections

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