MolNFT v1 · #120079 · protein

LYS48-linked di-ubiquitin

5GOI: “LYS48-linked di-ubiquitin”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #120079 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GOI
Type: protein
Length: 304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; D-ubiquitin
UniProt: P0CG47
Pockets: 3 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ubiquitin	protein	76	24% helix, 34% strand	P0CG47
C, D	D-ubiquitin	protein	76	25% helix, 33% strand	—

Pockets

3 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	57	0.58	0.91	21	empty
2	191	0.47	0.76	29	empty
3	128	0.41	0.75	20	empty

Interfaces

4 interfaces between chains.

C–D · 622 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 550 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 230 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 172 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 138 d-amino, 2 modified (D-amino acid, nonstandard).

Compared structures

5GOI · Lys48-linked di-ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00

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 P0CG47
Elsewhere: RCSB PDB 5GOI · PDBe 5GOI · UniProt P0CG47

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