Research workbench

Structure of an ubiquitin complex

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

PDB: 4NQK
Type: protein
Length: 1,187 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ATP-dependent RNA helicase DDX58; Ubiquitin
EC: 3.6.4.13
UniProt: O95786, P0CG48
Pockets: 15 · best druggability 0.90

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Probable ATP-dependent RNA helicase DDX58 (EC 3.6.4.13)	protein	188	72% helix, 0% strand	O95786
E	Ubiquitin	protein	72	21% helix, 32% strand	P0CG48
F, J	Ubiquitin	protein	73	21% helix, 30% strand	P0CG48
G, I	Ubiquitin	protein	71	17% helix, 32% strand	P0CG48
H	Ubiquitin	protein	75	16% helix, 31% strand	P0CG48

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1058	0.90	0.92	124	empty
2	256	0.77	0.90	32	empty
3	363	0.76	0.86	48	empty
4	93	0.74	0.96	22	empty
5	84	0.73	0.96	18	empty

Interfaces

17 interfaces between chains.

A–B · 1087 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1076 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 1022 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 941 Å² buried · 8 hydrogen bonds · protein-protein
C–H · 708 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4NQK · Structure of an Ubiquitin complex · the same entry in another collection · chain D against D, TM-score 1.00
O95786 · AlphaFold monomer V2.0 prediction for antiviral innate immune response receptor rig-I… · a predicted model of the same protein · chain C against A, TM-score 0.96

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 O95786
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 4NQK · PDBe 4NQK · UniProt O95786 · UniProt P0CG48

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