MolNFT v1 · #63357 · protein

Sf-1 lbd bound by phosphatidylcholine

3F7D · Nuclear receptor sf-1: “Sf-1 lbd bound by phosphatidylcholine”. X-ray diffraction, 1 ligand (P42), 4 pockets (best druggability 0.83). MolNFT v1 #63357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3F7D
Type: protein
Length: 248 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear receptor sf-1; Peroxisome proliferator-activated receptor gamma coactivator…
UniProt: Q812G5, O70343
Ligands: P42
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear receptor sf-1	protein	238	68% helix, 3% strand	Q812G5
B	Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	protein	10	70% helix, 0% strand	O70343

Ligands and binding sites

P42 · (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	539	0.83	0.89	39	P42
2	151	0.69	0.89	25	empty
3	137	0.47	0.78	19	empty
4	82	0.32	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 532 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

3F7D · SF-1 LBD bound by phosphatidylcholine · the same entry in another collection · chain A against A, TM-score 1.00
O70343 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain B against A, TM-score 0.81

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 Q812G5
Every structure of UniProt O70343
Elsewhere: RCSB PDB 3F7D · PDBe 3F7D · UniProt Q812G5 · UniProt O70343

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