MolNFT v1 · #53991 · protein

NEDD4 hect structure

2XBF · E3 ubiquitin-protein ligase NEDD4: “NEDD4 hect structure”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.58). MolNFT v1 #53991 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XBF
Type: protein
Length: 375 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase NEDD4
EC: 6.3.2.-
UniProt: P46934
Ligands: CA
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-)	protein	375	50% helix, 14% strand	P46934

Ligands and binding sites

CA · Calcium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	314	0.58	0.77	30	empty
2	203	0.46	0.74	29	empty
3	117	0.44	0.77	30	empty
4	122	0.44	0.77	16	empty
5	56	0.27	0.73	10	EDO

Compared structures

2XBF · Nedd4 HECT structure · the same entry in another collection · chain A against A, TM-score 1.00
P46934 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase NEDD4 (P46934) · a predicted model of the same protein · chain A against A, TM-score 0.71

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P46934
Elsewhere: RCSB PDB 2XBF · PDBe 2XBF · UniProt P46934

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