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C-terminal domain of VPS54 subunit of the garp complex

Analyse C-terminal domain of VPS54 subunit of the garp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3N1B
Type: protein
Length: 263 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 54
UniProt: Q5SPW0
Pockets: 1 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 54	protein	131	72% helix, 0% strand	Q5SPW0
B	Vacuolar protein sorting-associated protein 54	protein	132	64% helix, 0% strand	Q5SPW0

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	729	0.68	0.76	89	empty

Interfaces

1 interface between chains.

A–B · 520 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

3N1B · C-terminal domain of Vps54 subunit of the GARP complex · 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 0.94

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 3N1B · PDBe 3N1B · UniProt Q5SPW0

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