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Cyclic Lys48-linked triubiquitin

Analyse Cyclic Lys48-linked triubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CAP
Type: protein
Length: 228 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.33
Source: Homo sapiens
Molecule: Ubiquitin
UniProt: P0CG47
Ligands: ZN
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · resolution 1.33 · 1 distinct chain · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ubiquitin	protein	76	24% helix, 34% strand	P0CG47

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	603	0.76	0.82	57	ZN
2	171	0.53	0.79	29	ZN

Interfaces

3 interfaces between chains.

B–C · 398 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 334 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 304 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 isopeptide (isopeptide).

Compared structures

7CAP · Cyclic LYS48-linked triubiquitin · 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 7CAP · PDBe 7CAP · UniProt P0CG47

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