Research workbench
Torpedo californica acetylcholinesterase in complex with a non hydrolysable substrate analogue, 4-oxo-N,N,N- trimethylpentanaminium - orthorhombic space group - dataset D at 100K
Analyse Torpedo californica acetylcholinesterase in complex with a non hydrolysable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VJB
- Type
- protein
- Length
- 1,060 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
- CCD, NAG, CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 528 | 38% helix, 17% strand | P04058 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 38% helix, 17% strand | P04058 |
Ligands and binding sites
- CCD · (4R)-4-hydroxy-N,N,N-trimethylpentan-1-aminium · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.76 | 0.88 | 36 | CCD |
| 2 | 330 | 0.75 | 0.86 | 39 | CCD |
| 3 | 349 | 0.58 | 0.76 | 34 | empty |
| 4 | 332 | 0.58 | 0.76 | 35 | empty |
| 5 | 169 | 0.48 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 2VJB · Torpedo Californica Acetylcholinesterase In Complex With A Non Hydrolysable Substrate… · 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 2VJB · PDBe 2VJB · UniProt P04058
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