Research workbench

Human ubiquitin in the P1 space group

Analyse Human ubiquitin in the P1 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DK8
Type: protein
Length: 151 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.32
Source: Homo sapiens
Molecule: Polyubiquitin-B
UniProt: P0CG47
Ligands: MG
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · resolution 1.32 · 2 distinct chains · 24% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyubiquitin-B	protein	76	24% helix, 37% strand	P0CG47
B	Polyubiquitin-B	protein	75	24% helix, 36% strand	P0CG47

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

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	50	0.30	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 481 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5DK8 · Human ubiquitin in the P1 space group · the same entry in another collection · chain A against A, TM-score 1.00
P0CG47 · AlphaFold monomer V2.0 prediction for polyubiquitin-B (P0CG47) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 5DK8 · PDBe 5DK8 · UniProt P0CG47

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