6NXK: Ubiquitin binding variants

Ubiquitin binding variants. Determined by X-ray diffraction at 2.2 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,519
Mol. weight: 37.67 kDa
Released: 15 Jan 2020

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

Secondary structure: helices and β-sheets

6NXK contains 17 α-helices and 20 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: 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

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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	746-765	20
β-strand	768	1	5
α-helix	770-780	11
α-helix	785-787	3
α-helix	792-804	13
β-strand	809-811	3	5
β-strand	814-816	3	5
α-helix	817-819	3

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	747-765	19
β-strand	768-769	2	6
α-helix	770-783	14
α-helix	785-787	3
α-helix	792-804	13
β-strand	809-811	3	6
β-strand	814-816	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-C	A, B	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Anaphase-promoting complex subunit 2	C, D	protein	90	Homo sapiens	Q9UJX6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6NXK_1 Polyubiquitin-C (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (C, D), FASTA

>6NXK_2 Anaphase-promoting complex subunit 2 (chains C, D)
GSESDSGMASQADQKEEELLLFWTYIQAMLTNLESLSLDRIYNMLRMFVVTGPALAEIDL
QELQGYLQKKVRDQQLVYSAGVYRLPKNCS

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 P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
4HK2 1.4 Å, U7Ub25.2540
9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant

Browse structure collections

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