5GOI: Lys48-linked di-ubiquitin

Lys48-linked di-ubiquitin. Determined by X-ray diffraction at 1.59 Å resolution. Released 2 Nov 2016.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,628
Mol. weight: 34.26 kDa
Released: 2 Nov 2016

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

Secondary structure: helices and β-sheets

5GOI contains 15 α-helices and 28 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: 5 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
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1
α-helix	73-75	3

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	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

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	56-59	4
β-strand	66-71	6	5

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	12-16	5	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
α-helix	57-59	3
β-strand	66-71	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
D-ubiquitin	C, D	protein	76	Homo sapiens	P62987 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5GOI_1 Ubiquitin (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (C, D), FASTA

>5GOI_2 D-ubiquitin (chains C, D)
LQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Monomer/Oligomer Quasi-Racemic Protein Crystallography. Gao, S., Pan, M., Zheng, Y. et al. J Am Chem Soc (2016) 138:14497-14502. DOI 10.1021/jacs.6b09545 · 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

About this viewer

MolViewer shows 5GOI 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.