Research workbench

Structure of LPG2148/UBE2N-ub complex

Analyse Structure of LPG2148/UBE2N-ub complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LP2
Type: protein
Length: 606 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein LPG2148; Ubiquitin; Ubiquitin-conjugating enzyme E2 N
EC: 2.3.2.23
UniProt: Q5ZTL3, P0CG47, P61088
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein LPG2148	protein	384	52% helix, 14% strand	Q5ZTL3
C	Ubiquitin	protein	73	25% helix, 32% strand	P0CG47
D	Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23)	protein	149	33% helix, 17% strand	P61088

Pockets

6 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	472	0.77	0.85	64	empty
2	642	0.71	0.79	81	empty
3	58	0.70	0.97	25	empty
4	324	0.61	0.78	49	empty
5	199	0.60	0.81	29	empty

Interfaces

3 interfaces between chains.

A–C · 1478 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1474 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 197 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6LP2 · Structure of Lpg2148/UBE2N-Ub complex · the same entry in another collection · chain A against A, TM-score 1.00
P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain D against A, TM-score 0.94

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 Q5ZTL3
Every structure of UniProt P0CG47
Every structure of UniProt P61088
Elsewhere: RCSB PDB 6LP2 · PDBe 6LP2 · UniProt Q5ZTL3 · UniProt P0CG47 · UniProt P61088

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