Research workbench

Structure of NEDD4L WW3 domain

Analyse Structure of NEDD4L WW3 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LP2
Type: protein
Length: 141 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase; Angiomotin
EC: 2.3.2.26
UniProt: A0A6Q8PG51, Q4VCS5
Ligands: SO4
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	E3 ubiquitin-protein ligase (EC 2.3.2.26)	protein	33	0% helix, 42% strand	A0A6Q8PG51
B	Angiomotin	protein	11	27% helix, 0% strand	Q4VCS5
D	Angiomotin	protein	12	25% helix, 0% strand	Q4VCS5
E	E3 ubiquitin-protein ligase (EC 2.3.2.26)	protein	37	0% helix, 35% strand	A0A6Q8PG51
F	Angiomotin	protein	15	20% helix, 0% strand	Q4VCS5

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains E, F, D
GOL · Glycerol · additive · 2 copies · chains C, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.65	0.89	36	empty

Interfaces

11 interfaces between chains.

E–F · 552 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 529 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 489 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 382 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 327 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7LP2 · Structure of Nedd4L WW3 domain · the same entry in another collection · chain C against C, TM-score 1.00
Q4VCS5 · AlphaFold monomer V2.0 prediction for angiomotin (Q4VCS5) · a predicted model of the same protein · chain B against A, TM-score 0.35

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 A0A6Q8PG51
Every structure of UniProt Q4VCS5
Elsewhere: RCSB PDB 7LP2 · PDBe 7LP2 · UniProt A0A6Q8PG51 · UniProt Q4VCS5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.