4BE8: NEDD4 HECT A889F structure

Name: PDB 4BE8: NEDD4 HECT A889F structure
Published: 2013-05-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

NEDD4 HECT A889F structure. Determined by X-ray diffraction at 3.0 Å resolution. Released 1 May 2013.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 3,124
Mol. weight: 45.71 kDa
Released: 1 May 2013

Explore 4BE8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BE8 contains 23 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: 23 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	522-532	11
β-strand	542-547	6	1
α-helix	552-560	9
α-helix	566-570	5
β-strand	572-577	6	1
α-helix	585-600	16
α-helix	603-605	3
β-strand	608-610	3	2
β-strand	618-620	3	2
α-helix	624-626	3
α-helix	630-646	17
β-strand	655	1	2
α-helix	657-663	7
α-helix	670-675	6
α-helix	678-689	12
α-helix	692-695	4
β-strand	698	1	3
β-strand	700	1	4
α-helix	703-706	4
β-strand	713	1	4
β-strand	722	1	3
α-helix	728-736	9
α-helix	737-741	5
α-helix	745-756	12
α-helix	761-764	4
α-helix	769-776	8
α-helix	784-789	6
β-strand	791-794	4	5
α-helix	802-813	12
α-helix	816-826	11
α-helix	832-833	2
β-strand	841-842	2	6
β-strand	845-846	2	6
β-strand	849-853	5	5
α-helix	860-861	2
β-strand	862-864	3	5
β-strand	869-872	4	5
α-helix	878-889	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase NEDD4	A	protein	385	HOMO SAPIENS	P46934 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BE8_1 E3 UBIQUITIN-PROTEIN LIGASE NEDD4 (chains A)
GPLGSRDYKRKYEFFRRKLKKQNDIPNKFEMKLRRATVLEDSYRRIMGVKRADFLKARLW
IEFDGEKGLDYGGVAREWFFLISKEMFNPYYGLFEYSATDNYTLQINPNSGINPDHLSYF
KFIGRVAGMAVYHGKLLDGFFIRPFYKMMLHKPITLHDMESVDSEYYNSLRWILENDPTE
LDLRFIIDEELFGQTHQHELKNGGSEIVVTNKNKKEYIYLVIQWRFVNRIQKQMAAFKEG
FFELIPQDLIKIFDENELELLMSGLGDVDVNDWREHTKYKNGYSANHQVIQWFWKAVLMM
DSEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQSFTVEQWGTPEKLPRAHTCFNRLDLPP
YESFEELWDKLQMFIENTQGFDGVD

Primary citation

Structure of a Ubiquitin-Loaded Hect Ligase Reveals the Molecular Basis for Catalytic Priming. Maspero, E., Valentini, E., Mari, S. et al. Nat Struct Mol Biol (2013) 20:696. DOI 10.1038/NSMB.2566 · PubMed

Other PDB entries of the same protein (UniProt P46934 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N7F 1.1 Å, Crystal structure of 3rd WW domain of human Nedd4-1
4N7H 1.7 Å, Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of…
3B7Y 1.8 Å, Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4
9H9O 2.12 Å, Crystal structure of NEDD4 HECT domain in complex with norclomipramine
9H9T 2.17 Å, Crystal structure of NEDD4 HECT domain in complex with covalent inhibitor
5C91 2.44 Å, NEDD4 HECT with covalently bound indole-based inhibitor
2XBF 2.5 Å, Nedd4 HECT structure
4BBN 2.51 Å, NEDD4 HECT-Ub:Ub complex
2XBB 2.68 Å, Nedd4 HECT:Ub complex
5C7J 3.0 Å, Crystal structure of NEDD4 with a ub variant
2KPZ Human NEDD4 3RD WW Domain Complex with The Human T-cell Leukemia virus 1 GAG-Pro…
2KQ0 Human NEDD4 3rd WW Domain Complex with Ebola Zaire Virus Matrix Protein VP40 Derived…

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