Research workbench
Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in complex with Pam3
Analyse Cryo-EM structure of apolipoprotein N-acyltransferase Lnt from E. coli in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B0P
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.86
- Source
- Escherichia coli K-12; SYNTHETIC CONSTRUCT
- Molecule
- Apolipoprotein N-acyltransferase; Pam3-SKKKK
- EC
- 2.3.1.-
- UniProt
- P23930
- Ligands
- IG7
- Pockets
- 3 · best druggability 0.79
Structure
electron microscopy · resolution 2.86 · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 505 | 48% helix, 15% strand | P23930 |
| B | Pam3-SKKKK | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- IG7 · [(2~{S})-3-[(2~{S})-3-azanyl-2-(hexadecanoylamino)-3-oxidanylidene-propyl]sulfanyl-2-hexadecanoyloxy-propyl] hexadecanoate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.79 | 0.83 | 56 | IG7 |
| 2 | 168 | 0.56 | 0.81 | 28 | empty |
| 3 | 60 | 0.32 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 480 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- P23930 · AlphaFold monomer V2.0 prediction for apolipoprotein N-acyltransferase (P23930) · a predicted model of the same protein · chain A 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 8B0P · PDBe 8B0P · UniProt P23930
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