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Vps54 C-terminal domain

Analyse Vps54 C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3N1E
Type: protein
Length: 281 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.702
Source: Mus musculus
Molecule: Vacuolar protein sorting-associated protein 54
UniProt: Q5SPW0
Ligands: MG
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · resolution 1.702 · 2 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 54	protein	140	72% helix, 0% strand	Q5SPW0
B	Vacuolar protein sorting-associated protein 54	protein	141	75% helix, 0% strand	Q5SPW0

Ligands and binding sites

MG · Magnesium ion · metal · 5 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	168	0.46	0.75	28	MG
2	199	0.45	0.73	27	GOL
3	70	0.30	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 600 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3N1E · VPS54 C-terminal domain · the same entry in another collection · chain A against A, TM-score 1.00
Q5SPW0 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 54… · a predicted model of the same protein · chain A against A, TM-score 0.90

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 Q5SPW0
Elsewhere: RCSB PDB 3N1E · PDBe 3N1E · UniProt Q5SPW0

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