MolNFT v1 · #127771 · protein
Structure of the membrane integral lipoprotein N-acyltransferase lnt from E. COLI
5N6H · Apolipoprotein N-acyltransferase: “Structure of the membrane integral lipoprotein N-acyltransferase lnt from E. COLI”. X-ray diffraction, 9 pockets (best druggability 0.76). MolNFT v1 #127771 on GenesisL1: 3D structure, binding…
- PDB
- 5N6H
- Type
- protein
- Length
- 1,001 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 · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 503 | 50% helix, 16% strand | P23930 |
| B | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 498 | 51% helix, 17% strand | P23930 |
Ligands and binding sites
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 18 copies · chains A, B
- GOL · Glycerol · additive · 13 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 | 763 | 0.76 | 0.80 | 63 | empty |
| 2 | 770 | 0.75 | 0.79 | 62 | empty |
| 3 | 205 | 0.61 | 0.82 | 27 | empty |
| 4 | 216 | 0.61 | 0.82 | 26 | empty |
| 5 | 83 | 0.37 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5N6H · Structure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli · 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 5N6H · PDBe 5N6H · UniProt P23930
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