6NXL: Ubiquitin binding variants

Ubiquitin binding variants. Determined by X-ray diffraction at 2.8 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 8
Atoms: 4,490
Mol. weight: 71.17 kDa
Released: 15 Jan 2020

Explore 6NXL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NXL contains 31 α-helices and 56 β-strands across 8 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-17	17	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	65	1	3
β-strand	66-71	6	1
β-strand	73	1	1

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-16	15	1
β-strand	22	1	4
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	4
α-helix	57-59	3
β-strand	65	1	5
β-strand	66-71	6	1
β-strand	73	1	1

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-16	15	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
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	65	1	1
β-strand	66-71	6	5

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-16	15	5
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	7
β-strand	66-71	6	5

Chain E: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1-17	17	1
β-strand	22	1	8
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	8
α-helix	57-59	3
β-strand	66-71	6	1

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-16	15	1
β-strand	22	1	9
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	9
α-helix	57-59	3
β-strand	66-71	6	1
β-strand	72	1	5

Chain G: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-17	16	3
β-strand	22	1	10
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	10
α-helix	57-59	3
β-strand	66-71	6	3
β-strand	72	1	1

Chain H: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-16	16	3
β-strand	22	1	11
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	11
α-helix	57-59	3
β-strand	65	1	1
β-strand	66-71	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-B	A, B, C, D, E, F, G, H	protein	80	Homo sapiens	B4DV12 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>6NXL_1 Polyubiquitin-B (chains A, B, C, D, E, F, G, H)
GSGGSGMQIFVDTVQWKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR
TLSDYNIQKESALILLLTLR

Primary citation

Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Watson, E.R., Grace, C.R.R., Zhang, W. et al. Proc Natl Acad Sci U S A (2019) 116:17280-17289. DOI 10.1073/pnas.1902889116 · PubMed

Other PDB entries of the same protein (UniProt B4DV12 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SVI 1.15 Å, Ubiquitin variant i53:Mutant L67H with 53BP1 Tudor domain
8SVH 1.16 Å, Ubiquitin variant i53 mutant L67R bound to 53BP1 Tudor Domain
8SVG 1.21 Å, Ubiquitin variant i53 in complex with 53BP1 Tudor domain
8SVJ 1.5 Å, Ubiquitin variant i53: mutant VHH with 53BP1 Tudor domain

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