MolNFT v1 · #167887 · protein
Cryo-EM structure of human diacylglycerol O-acyltransferase 1
6VYI: “Cryo-EM structure of human diacylglycerol O-acyltransferase 1”. Electron microscopy, 1 ligand (6OU), 9 pockets (best druggability 0.86). MolNFT v1 #167887 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VYI
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol O-acyltransferase 1
- EC
- 2.3.1.20
- UniProt
- O75907
- Ligands
- 6OU
- Pockets
- 9 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20) | protein | 406 | 70% helix, 0% strand | O75907 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.86 | 0.86 | 83 | empty |
| 2 | 984 | 0.85 | 0.86 | 85 | empty |
| 3 | 1130 | 0.85 | 0.85 | 82 | 6OU |
| 4 | 123 | 0.42 | 0.76 | 21 | empty |
| 5 | 125 | 0.42 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3056 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6VYI · Cryo-EM structure of human diacylglycerol O-acyltransferase 1 · the same entry in another collection · chain A against A, TM-score 1.00
- O75907 · AlphaFold monomer V2.0 prediction for diacylglycerol O-acyltransferase 1 (O75907) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 O75907
- Elsewhere: RCSB PDB 6VYI · PDBe 6VYI · UniProt O75907
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