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Crystal structure of spf bound to 2,3-oxidosqualene

Analyse Crystal structure of spf bound to 2,3-oxidosqualene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OMJ
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: 2TX, CL, SO4
Pockets: 10 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	SEC14-like protein 2	protein	274	52% helix, 11% strand	O76054

Ligands and binding sites

2TX · (3S)-2,2-dimethyl-3-[(3E,7E,11E,15E)-3,7,12,16,20-pentamethylhenicosa-3,7,11,15,19-pentaen-1-yl]oxirane · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 9 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B

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

Pockets

10 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	394	0.88	0.95	45	2TX
2	396	0.87	0.95	48	2TX
3	170	0.61	0.84	25	empty
4	176	0.61	0.83	25	empty
5	161	0.48	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 389 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4OMJ · Crystal structure of SPF bound to 2,3-oxidosqualene · 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 4OMJ · PDBe 4OMJ · UniProt O76054

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