Research workbench
Torpedo californica ache in complex with indolic multi-target directed ligand
Analyse Torpedo californica ache in complex with indolic multi-target directed ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EZH
- Type
- protein
- Length
- 1,064 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
- C6H, NAG
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylcholinesterase (EC 3.1.1.7) | protein | 532 | 39% helix, 17% strand | P04058 |
Ligands and binding sites
- C6H · 1-(7-chloranyl-4-methoxy-1~{H}-indol-5-yl)-3-[1-(cyclohexylmethyl)piperidin-4-yl]propan-1-one · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.78 | 0.88 | 32 | C6H |
| 2 | 376 | 0.77 | 0.87 | 39 | C6H |
| 3 | 345 | 0.59 | 0.77 | 35 | empty |
| 4 | 347 | 0.58 | 0.76 | 35 | empty |
| 5 | 151 | 0.48 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 954 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6EZH · Torpedo californica AChE in complex with indolic multi-target directed ligand · 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 6EZH · PDBe 6EZH · UniProt P04058
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