Research workbench
Thioester acyl-intermediate of Apolipoprotein N-acyltransferase (Lnt)
Analyse Thioester acyl-intermediate of Apolipoprotein N-acyltransferase (Lnt) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NWR
- Type
- protein
- Length
- 999 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Escherichia coli (strain K12)
- Molecule
- Apolipoprotein N-acyltransferase
- EC
- 2.3.1.-
- UniProt
- P23930
- Ligands
- D12
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · resolution 3.5 · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 488 | 49% helix, 15% strand | P23930 |
| B | Apolipoprotein N-acyltransferase (EC 2.3.1.-) | protein | 511 | 48% helix, 15% strand | P23930 |
Ligands and binding sites
- D12 · Dodecane · ligand · chains B
- LMT · Dodecyl-beta-D-maltoside · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.79 | 0.81 | 71 | empty |
| 2 | 474 | 0.71 | 0.80 | 44 | empty |
| 3 | 230 | 0.68 | 0.85 | 42 | D12 |
| 4 | 160 | 0.56 | 0.81 | 26 | empty |
| 5 | 57 | 0.36 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 593 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6NWR · Thioester acyl-intermediate of apolipoprotein N-acyltransferase (lnt) · 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 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 6NWR · PDBe 6NWR · UniProt P23930
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