MolNFT v1 · #153058 · protein

Semi-open conformation E3 ligase

6J1Y · NEDD4-like E3 ubiquitin-protein ligase WWP1: “Semi-open conformation E3 ligase”. X-ray diffraction, 11 pockets (best druggability 0.79). MolNFT v1 #153058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6J1Y
Type: protein
Length: 866 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NEDD4-like E3 ubiquitin-protein ligase WWP1
EC: 2.3.2.26
UniProt: Q9H0M0
Pockets: 11 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NEDD4-like E3 ubiquitin-protein ligase WWP1 (EC 2.3.2.26)	protein	401	52% helix, 13% strand	Q9H0M0
B	NEDD4-like E3 ubiquitin-protein ligase WWP1 (EC 2.3.2.26)	protein	465	44% helix, 13% strand	Q9H0M0

Ligands and binding sites

GOL · Glycerol · additive · chains B

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.79	0.81	97	empty
2	732	0.78	0.83	73	empty
3	199	0.61	0.82	36	empty
4	77	0.54	0.85	18	empty
5	130	0.53	0.81	27	empty

Interfaces

1 interface between chains.

A–B · 946 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6J1Y · Semi-open conformation E3 ligase · the same entry in another collection · chain A against A, TM-score 1.00
Q9H0M0 · AlphaFold monomer V2.0 prediction for NEDD4-like E3 ubiquitin-protein ligase WWP1 (Q9H0M0) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9H0M0
Elsewhere: RCSB PDB 6J1Y · PDBe 6J1Y · UniProt Q9H0M0

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