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HNF4A ligand binding domain with bound fatty acid

Analyse HNF4A ligand binding domain with bound fatty acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1M7W
Type: protein
Length: 882 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepatocyte nuclear factor 4-alpha
UniProt: P22449
Ligands: DAO
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hepatocyte nuclear factor 4-alpha	protein	223	64% helix, 3% strand	P22449
B	Hepatocyte nuclear factor 4-alpha	protein	218	69% helix, 3% strand	P22449
C	Hepatocyte nuclear factor 4-alpha	protein	220	64% helix, 3% strand	P22449
D	Hepatocyte nuclear factor 4-alpha	protein	221	66% helix, 3% strand	P22449

Ligands and binding sites

DAO · Lauric acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	169	0.81	0.96	24	DAO
2	166	0.81	0.96	27	DAO
3	146	0.78	0.94	22	DAO
4	260	0.77	0.89	41	DAO
5	783	0.73	0.78	70	empty

Interfaces

5 interfaces between chains.

A–B · 1207 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1175 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 792 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 112 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 96 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1M7W · HNF4a ligand binding domain with bound fatty acid · the same entry in another collection · chain D against D, TM-score 1.00
P22449 · AlphaFold monomer V2.0 prediction for hepatocyte nuclear factor 4-alpha (P22449) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P22449
Elsewhere: RCSB PDB 1M7W · PDBe 1M7W · UniProt P22449

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