Research workbench

Crystal structure of spf bound to squalene

Analyse Crystal structure of spf bound to squalene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OMK
Type: protein
Length: 548 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SEC14-like protein 2
UniProt: O76054
Ligands: SQL, SO4, CL
Pockets: 11 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	SEC14-like protein 2	protein	274	52% helix, 12% strand	O76054

Ligands and binding sites

SQL · (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2, 6,10,14,18,22-hexaene · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 6 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
IPA · Isopropyl alcohol · additive · 2 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	403	0.87	0.95	48	SQL, IPA
2	408	0.87	0.95	48	SQL, IPA
3	166	0.61	0.83	23	empty
4	140	0.55	0.82	22	empty
5	170	0.49	0.77	22	empty

Interfaces

1 interface between chains.

A–B · 388 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4OMK · Crystal structure of SPF bound to squalene · the same entry in another collection · chain A against A, TM-score 1.00
O76054 · AlphaFold monomer V2.0 prediction for SEC14-like protein 2 (O76054) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O76054
Elsewhere: RCSB PDB 4OMK · PDBe 4OMK · UniProt O76054

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