2ONI: E3 ubiquitin-protein ligase NEDD4-like protein

Name: PDB 2ONI: Catalytic Domain of the Human NEDD4-like E3 Ligase
Published: 2007-04-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Catalytic Domain of the Human NEDD4-like E3 Ligase. Determined by X-ray diffraction at 2.2 Å resolution. Released 17 Apr 2007.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,269
Mol. weight: 47.27 kDa
Released: 17 Apr 2007

Explore 2ONI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ONI contains 26 α-helices and 15 β-strands across 1 chain. 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: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	574-587	14
β-strand	597-602	6	1
α-helix	604-606	3
α-helix	607-617	11
α-helix	621-625	5
β-strand	627-632	6	1
α-helix	640-655	16
α-helix	658-660	3
β-strand	663-665	3	2
β-strand	673-675	3	2
α-helix	679-682	4
α-helix	686-703	18
α-helix	705-707	3
β-strand	711	1	2
α-helix	713-719	7
α-helix	722-724	3
α-helix	727-730	4
α-helix	734-745	12
α-helix	749-751	3
β-strand	754	1	3
β-strand	756-761	6	4
β-strand	764-769	6	4
α-helix	774-776	3
β-strand	778	1	3
α-helix	784-796	13
α-helix	801-814	14
α-helix	817-820	4
α-helix	825-833	9
α-helix	840-845	6
β-strand	848-850	3	5
α-helix	858-869	12
α-helix	872-883	12
α-helix	893-895	3
β-strand	897-898	2	6
β-strand	901-902	2	6
β-strand	906-909	4	5
α-helix	916-917	2
β-strand	918-920	3	5
α-helix	921-923	3
β-strand	925-928	4	5
α-helix	934-945	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase NEDD4-like protein	A	protein	392	Homo sapiens	Q96PU5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2ONI_1 E3 ubiquitin-protein ligase NEDD4-like protein (chains A)
MHHHHHHSSGRENLYFQGSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRI
MSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQI
NPNSGLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSE
YYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQWR
FVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDWRQHSIYKNGYCP
NHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQLFTIEQWGSPEK
LPRAHTCFNRLDLPPYETFEDLREKLLMAVEN

Primary citation

NEDD4-like E3 Ubiquitin-protein Ligase. Walker, J.R., Avvakumov, G.V., Xue, S. et al. To be published.

Other PDB entries of the same protein (UniProt Q96PU5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7LP1 1.35 Å, Structure of Nedd4L WW3 domain
7LP3 1.61 Å, Structure of Nedd4L WW3 domain
6ZBT 1.8 Å, Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser342
2NSQ 1.85 Å, Crystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like…
7LP2 1.88 Å, Structure of Nedd4L WW3 domain
6ZC9 1.9 Å, Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448
7NMZ 2.3 Å, Structure of 14-3-3 eta in complex with Nedd4-2(335-455) containing two 14-3-3 binding…
5HPK 2.43 Å, System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes:…
9Z5Q 3.06 Å, HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11
3JW0 3.1 Å, E2~Ubiquitin-HECT
3JVZ 3.3 Å, E2~Ubiquitin-HECT
9GIK 3.58 Å, Full-lenght Nedd4-2 E3 ubiquitin ligase

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