MolNFT v1 · #13930 · protein

Lipid-protein interactions in lipovitellin

1LSH · Lipovitellin (lv-1N, lv-1C): “Lipid-protein interactions in lipovitellin”. X-ray diffraction, 2 ligands (UPL, PLD), 14 pockets (best druggability 0.78). MolNFT v1 #13930 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1LSH
Type: protein
Length: 1,129 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipovitellin (lv-1N, lv-1C); Lipovitellin (lv-2)
UniProt: Q91062
Ligands: UPL, PLD
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipovitellin (lv-1N, lv-1C)	protein	955	31% helix, 37% strand	Q91062
B	Lipovitellin (lv-2)	protein	174	14% helix, 50% strand	Q91062

Ligands and binding sites

UPL · Unknown branched fragment of phospholipid · ligand · 43 copies · chains A, B
PLD · di-heneicosanoyl phosphatidyl choline · ligand · 7 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	791	0.78	0.81	87	PLD
2	85	0.76	0.98	38	empty
3	210	0.72	0.87	35	UPL
4	192	0.67	0.86	40	empty
5	177	0.62	0.84	32	empty

Interfaces

1 interface between chains.

A–B · 1056 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, cyclization).

Compared structures

1LSH · Lipid-protein interactions in lipovitellin · the same entry in another collection · chain A against A, TM-score 1.00
Q91062 · AlphaFold monomer V2.0 prediction for vitellogenin (Q91062) · 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 Q91062
Elsewhere: RCSB PDB 1LSH · PDBe 1LSH · UniProt Q91062

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