MolNFT v1 · #120080 · protein

LYS63-linked di-ubiquitin

5GOJ: “LYS63-linked di-ubiquitin”. X-ray diffraction, 1 pocket (best druggability 0.33). MolNFT v1 #120080 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GOJ
Type: protein
Length: 151 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; D-ubiquitin
UniProt: P0CG47
Pockets: 1 · best druggability 0.33

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin	protein	75	24% helix, 35% strand	P0CG47
B	D-ubiquitin	protein	76	24% helix, 33% strand	—

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.33	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 330 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 69 d-amino, 1 modified (D-amino acid, nonstandard).

Compared structures

5GOJ · Lys63-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 5GOJ · PDBe 5GOJ · UniProt P0CG47

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