MolNFT v1 · #52951 · protein
Non-aged conjugate of torpedo californica acetylcholinesterase with soman (alternative refinement)
2WG2: “Non-aged conjugate of torpedo californica acetylcholinesterase with soman (alternative refinement)”. X-ray diffraction, 4 ligands (GD8, NAG, FUC), 6 pockets (best druggability 0.76). MolNFT v1 #52951 on GenesisL1: 3D structure…
- PDB
- 2WG2
- Type
- protein
- Length
- 532 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P04058
- Ligands
- GD8, NAG, FUC, CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 39% helix, 17% strand | P04058 |
Ligands and binding sites
- GD8 · (1R)-1,2,2-trimethylpropyl (S)-methylphosphinate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.76 | 0.87 | 37 | GD8, PG4 |
| 2 | 344 | 0.58 | 0.76 | 33 | empty |
| 3 | 128 | 0.45 | 0.77 | 18 | empty |
| 4 | 82 | 0.39 | 0.78 | 14 | empty |
| 5 | 60 | 0.31 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 2WG2 · Non-aged conjugate of torpedo californica acetylcholinesterase with soman (alternative… · the same entry in another collection · chain A against A, TM-score 1.00
- P04058 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P04058) · a predicted model of the same protein · 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 P04058
- Elsewhere: RCSB PDB 2WG2 · PDBe 2WG2 · UniProt P04058
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