MolNFT v1 · #150332 · protein

The structure of mouse astera (GRAMD1A) with 25-hydroxy cholesterol

6GQF · Gram domain-containing protein 1A: “The structure of mouse astera (GRAMD1A) with 25-hydroxy cholesterol”. X-ray diffraction, 1 ligand (HC3), 9 pockets (best druggability 0.81). MolNFT v1 #150332 on GenesisL1: 3D structure, binding…

PDB: 6GQF
Type: protein
Length: 666 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gram domain-containing protein 1A
UniProt: Q8VEF1
Ligands: HC3
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 27% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gram domain-containing protein 1A	protein	168	26% helix, 42% strand	Q8VEF1
B	Gram domain-containing protein 1A	protein	163	25% helix, 42% strand	Q8VEF1
C	Gram domain-containing protein 1A	protein	168	30% helix, 40% strand	Q8VEF1
D	Gram domain-containing protein 1A	protein	167	29% helix, 44% strand	Q8VEF1

Ligands and binding sites

HC3 · 25-hydroxycholesterol · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	418	0.81	0.89	45	HC3, GOL
2	1031	0.80	0.82	91	empty
3	411	0.79	0.87	41	HC3
4	439	0.76	0.84	46	HC3, GOL
5	698	0.75	0.81	75	empty

Interfaces

5 interfaces between chains.

A–B · 1073 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 737 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 692 Å² buried · 1 hydrogen bond · protein-protein
A–D · 255 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 208 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6GQF · The structure of mouse AsterA (GramD1a) with 25-hydroxy cholesterol · the same entry in another collection · chain D against D, TM-score 1.00
Q8VEF1 · AlphaFold monomer V2.0 prediction for protein aster-a (Q8VEF1) · 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 Q8VEF1
Elsewhere: RCSB PDB 6GQF · PDBe 6GQF · UniProt Q8VEF1

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