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Cyclic LYS48-linked tetraubiquitin

Analyse Cyclic LYS48-linked tetraubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ALB
Type: protein
Length: 304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin
UniProt: P0CG48
Ligands: SO4
Pockets: 1 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ubiquitin	protein	76	24% helix, 34% strand	P0CG48

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.83	0.92	53	empty

Interfaces

6 interfaces between chains.

A–B · 731 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 689 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 311 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 266 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 207 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 isopeptide (isopeptide).

Compared structures

3ALB · Cyclic Lys48-linked tetraubiquitin · 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 P0CG48
Elsewhere: RCSB PDB 3ALB · PDBe 3ALB · UniProt P0CG48

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