MolNFT v1 · #24594 · protein

A complex of the VPS23 uev with ubiquitin

1UZX · Vacuolar protein sorting-associated protein VPS23: “A complex of the VPS23 uev with ubiquitin”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.56). MolNFT v1 #24594 on GenesisL1: 3D structure, binding sites and…

PDB: 1UZX
Type: protein
Length: 214 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein VPS23; Ubiquitin
UniProt: P25604, P02248
Ligands: SO4
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein VPS23	protein	140	35% helix, 23% strand	P25604
B	Ubiquitin	protein	74	24% helix, 34% strand	P02248

Ligands and binding sites

SO4 · Sulfate ion · ion · chains B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A

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

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	169	0.56	0.81	31	empty
2	163	0.46	0.76	28	MES
3	90	0.45	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 678 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered, nonstandard).

Compared structures

1UZX · A complex of the Vps23 UEV with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
P25604 · AlphaFold monomer V2.0 prediction for suppressor protein STP22 of temperature-sensitive… · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P25604
Every structure of UniProt P02248
Elsewhere: RCSB PDB 1UZX · PDBe 1UZX · UniProt P25604 · UniProt P02248

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