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Structure of nevanimibe-bound human tetrameric ACAT1

Analyse Structure of nevanimibe-bound human tetrameric ACAT1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VUM
Type: protein
Length: 1,636 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sterol O-acyltransferase 1
EC: 2.3.1.26
UniProt: P35610
Ligands: CLR, OLA, ROV, COA, 3VV
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 1 distinct chain · 69% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Sterol O-acyltransferase 1 (EC 2.3.1.26)	protein	409	69% helix, 0% strand	P35610

Ligands and binding sites

CLR · Cholesterol · ligand · 10 copies · chains A, B, C, D
OLA · Oleic acid · ligand · 4 copies · chains A, B, C, D
ROV · nevanimibe · ligand · 4 copies · chains A, B, C, D
COA · Coenzyme A · ligand · 2 copies · chains A, C
3VV · S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3, 5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2, 4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) · ligand · 2 copies · chains B, D

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

Pockets

20 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	1150	0.89	0.89	74	CLR
2	1174	0.88	0.89	78	CLR
3	1008	0.86	0.87	87	OLA, ROV, COA
4	1069	0.86	0.87	81	OLA, 3VV, ROV
5	984	0.86	0.87	83	OLA, 3VV, ROV

Interfaces

3 interfaces between chains.

C–D · 1907 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1901 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 344 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6VUM · Structure of nevanimibe-bound human tetrameric ACAT1 · the same entry in another collection · chain A against A, TM-score 1.00
P35610 · AlphaFold monomer V2.0 prediction for sterol O-acyltransferase 1 (P35610) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P35610
Elsewhere: RCSB PDB 6VUM · PDBe 6VUM · UniProt P35610

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