3B7Y: E3 ubiquitin-protein ligase NEDD4

Name: PDB 3B7Y: Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4
Published: 2007-11-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4. Determined by X-ray diffraction at 1.8 Å resolution. Released 27 Nov 2007.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,553
Mol. weight: 35.58 kDa
Ligands: CA
Released: 27 Nov 2007

Explore 3B7Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B7Y contains 10 α-helices and 22 β-strands across 2 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	108-110	3	1
β-strand	119-129	11	1
β-strand	142-150	9	2
β-strand	154-160	7	2
α-helix	161-164	4
β-strand	174-180	7	1
β-strand	186-193	8	2
α-helix	199-200	2
β-strand	201-209	9	2
α-helix	214	1
β-strand	215	1	1
α-helix	216	1
α-helix	221-223	3
β-strand	227-230	4	1
β-strand	232	1	2
β-strand	243-250	8	1

Chain B: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	108-110	3	3
β-strand	119-129	11	3
α-helix	131-133	3
β-strand	142-150	9	4
β-strand	154-160	7	4
α-helix	161-164	4
β-strand	174-180	7	3
β-strand	186-193	8	4
α-helix	194-196	3
β-strand	202-209	8	4
α-helix	214	1
β-strand	215	1	3
α-helix	216	1
β-strand	227-230	4	3
β-strand	232	1	4
β-strand	243-250	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase NEDD4	A, B	protein	153	Homo sapiens	P46934 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3B7Y_1 E3 ubiquitin-protein ligase NEDD4 (chains A, B)
GMATCAVEVFGLLEDEENSRIVRVRVIAGIGLAKKDILGASDPYVRVTLYDPMNGVLTSV
QTKTIKKSLNPKWNEEILFRVHPQQHRLLFEVFDENRLTRDDFLGQVDVPLYPLPTENPR
LERPYTFKDFVLHPRSHKSRVKGYLRLKMTYLP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

C2 Domain of the Human E3 Ubiquitin-Protein Ligase NEDD4. Walker, J.R., Ruzanov, M., Butler-Cole, C. et al. To be published.

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…
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
4BE8 3.0 Å, NEDD4 HECT A889F structure
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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