MolNFT v1 · #178081 · protein
Lysophospholipid acyltransferase LPCAT3 in a complex with arachidonoyl-CoA
7F40: “Lysophospholipid acyltransferase LPCAT3 in a complex with arachidonoyl-CoA”. Electron microscopy, 2 ligands (3IX, PCW), 13 pockets (best druggability 0.85). MolNFT v1 #178081 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7F40
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LPCAT3
- UniProt
- A0A1L1RNG8
- Ligands
- 3IX, PCW
- Pockets
- 13 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | LPCAT3 | protein | 449 | 61% helix, 0% strand | A0A1L1RNG8 |
Ligands and binding sites
- 3IX · S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate · ligand · 2 copies · chains A, B
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.85 | 0.86 | 86 | 3IX |
| 2 | 1128 | 0.85 | 0.85 | 82 | 3IX |
| 3 | 278 | 0.70 | 0.85 | 37 | empty |
| 4 | 271 | 0.70 | 0.84 | 35 | empty |
| 5 | 543 | 0.65 | 0.76 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 280 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7F40 · Lysophospholipid acyltransferase LPCAT3 in a complex with Arachidonoyl-CoA · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1L1RNG8
- Elsewhere: RCSB PDB 7F40 · PDBe 7F40 · UniProt A0A1L1RNG8
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