MolNFT v1 · #54216 · protein
Torpedo californica acetylcholinesterase in complex with aflatoxin B1 (orthorhombic space group)
2XI4: “Torpedo californica acetylcholinesterase in complex with aflatoxin B1 (orthorhombic space group)”. X-ray diffraction, 4 ligands (AFT, NAG, K), 13 pockets (best druggability 0.76). MolNFT v1 #54216 on GenesisL1: 3D structure, binding…
- PDB
- 2XI4
- Type
- protein
- Length
- 1,062 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P04058
- Ligands
- AFT, NAG, K, CL
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 530 | 40% helix, 17% strand | P04058 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 38% helix, 17% strand | P04058 |
Ligands and binding sites
- AFT · Aflatoxin B1 · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.76 | 0.88 | 39 | AFT, PGE |
| 2 | 267 | 0.69 | 0.84 | 36 | AFT, PGE |
| 3 | 182 | 0.60 | 0.82 | 41 | PEG |
| 4 | 334 | 0.59 | 0.76 | 33 | empty |
| 5 | 339 | 0.58 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 980 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 2XI4 · Torpedo californica Acetylcholinesterase in Complex with Aflatoxin B1 (Orthorhombic Space… · 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 B 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 2XI4 · PDBe 2XI4 · UniProt P04058
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