5J8P: Lys27-linked diubiquitin

Lys27-linked diubiquitin. Determined by X-ray diffraction at 1.55 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,310
Mol. weight: 17.17 kDa
Ligands: MG
Released: 18 May 2016

Explore 5J8P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J8P contains 6 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.

Chains A and B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	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
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	A	protein	76	Homo sapiens	P62987 (AlphaFold model)
D-ubiquitin	B	protein	76	Homo sapiens	P62987 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5J8P_1 ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>5J8P_2 D-ubiquitin (chains B)
LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Structure of Lys27-linked diubiquitin. Pan, M., Gao, S., Zheng, Y. To be published.

Other PDB entries of the same protein (UniProt P62987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
4PIH 1.5 Å, X-ray crystal structure of the K33S mutant of ubiquitin
4PIJ 1.5 Å, X-ray crystal structure of the K11S/K63S double mutant of ubiquitin
5GOJ 1.55 Å, Lys63-linked di-ubiquitin
5GOI 1.59 Å, Lys48-linked di-ubiquitin
8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
5GOC 1.73 Å, Lys11-linked diubiquitin
29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
8QYX 1.78 Å, Human 60S ribosomal subunit
4HJK 1.78 Å, U7Ub7 Disulfide variant
5GO7 1.8 Å, Linear tri-ubiquitin

Browse structure collections

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