Research workbench

Spfh domain of mouse stomatin (crystal form 1)

Analyse Spfh domain of mouse stomatin (crystal form 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FVF
Type: protein
Length: 232 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Stomatin
UniProt: P54116
Ligands: CD
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Stomatin	protein	115	45% helix, 30% strand	P54116
B	Stomatin	protein	117	47% helix, 32% strand	P54116

Ligands and binding sites

CD · Cadmium ion · metal · 13 copies · chains A, B
ACT · Acetate ion · additive · chains A

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

Pockets

2 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	125	0.49	0.79	20	empty
2	111	0.46	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 692 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4FVF · SPFH domain of mouse stomatin (Crystal form 1) · the same entry in another collection · chain A against A, TM-score 1.00
P54116 · AlphaFold monomer V2.0 prediction for stomatin (P54116) · 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 P54116
Elsewhere: RCSB PDB 4FVF · PDBe 4FVF · UniProt P54116

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.