MolNFT v1 · #127773 · protein
Structure of the membrane integral lipoprotein N-acyltransferase lnt C387A mutant from E. COLI
5N6L · Apolipoprotein N-acyltransferase: “Structure of the membrane integral lipoprotein N-acyltransferase lnt C387A mutant from E. COLI”. X-ray diffraction, 9 pockets (best druggability 0.76). MolNFT v1 #127773 on GenesisL1: 3D structure…
- PDB
- 5N6L
- Type
- protein
- Length
- 997 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein N-acyltransferase
- EC
- 2.3.1.-
- UniProt
- P23930
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 506 | 49% helix, 15% strand | P23930 |
| B | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 491 | 51% helix, 17% strand | P23930 |
Ligands and binding sites
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 27 copies · chains A, B
- GOL · Glycerol · additive · 12 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.76 | 0.80 | 60 | OLC |
| 2 | 749 | 0.76 | 0.80 | 62 | empty |
| 3 | 212 | 0.59 | 0.81 | 27 | empty |
| 4 | 188 | 0.58 | 0.81 | 26 | empty |
| 5 | 179 | 0.46 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 55 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5N6L · Structure of the membrane integral lipoprotein N-acyltransferase Lnt C387A mutant from E.… · the same entry in another collection · chain A against A, TM-score 1.00
- P23930 · AlphaFold monomer V2.0 prediction for apolipoprotein N-acyltransferase (P23930) · a predicted model of the same protein · chain B 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 P23930
- Elsewhere: RCSB PDB 5N6L · PDBe 5N6L · UniProt P23930
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