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Ultraspiracle ligand binding domain from drosophila melanogaster

Analyse Ultraspiracle ligand binding domain from drosophila melanogaster in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HG4
Type: protein
Length: 1,436 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ultraspiracle
UniProt: P20153
Ligands: LPP
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F	Ultraspiracle	protein	240	67% helix, 3% strand	P20153
C, D	Ultraspiracle	protein	238	64% helix, 3% strand	P20153

Ligands and binding sites

LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 6 copies · chains A, B, D, C, E, F

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	537	0.84	0.89	39	LPP
2	522	0.83	0.88	35	LPP
3	508	0.83	0.88	35	LPP
4	533	0.83	0.88	36	LPP
5	481	0.82	0.88	35	LPP

Interfaces

8 interfaces between chains.

B–E · 556 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 553 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 547 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 529 Å² buried · 6 hydrogen bonds · protein-protein
E–F · 498 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1HG4 · Ultraspiracle ligand binding domain from Drosophila melanogaster · the same entry in another collection · chain F against F, TM-score 1.00
P20153 · AlphaFold monomer V2.0 prediction for protein ultraspiracle (P20153) · 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 P20153
Elsewhere: RCSB PDB 1HG4 · PDBe 1HG4 · UniProt P20153

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