MolNFT v1 · #15470 · protein
Crystal structure of the mouse acetylcholinesterase-propidium complex
1N5R: “Crystal structure of the mouse acetylcholinesterase-propidium complex”. X-ray diffraction, 3 ligands (PRM, NAG, FUC), 14 pockets (best druggability 0.77). MolNFT v1 #15470 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1N5R
- Type
- protein
- Length
- 1,070 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholinesterase
- EC
- 3.1.1.7
- UniProt
- P21836
- Ligands
- PRM, NAG, FUC
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 536 | 38% helix, 18% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 534 | 38% helix, 18% strand | P21836 |
Ligands and binding sites
- PRM · 3,8-diamino-5[3-(diethylmethylammonio)propyl]-6-phenylphenanthridinium · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- ACY · Acetic acid · additive · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.77 | 0.90 | 36 | ACY |
| 2 | 268 | 0.76 | 0.88 | 36 | PRM, ACY |
| 3 | 144 | 0.66 | 0.87 | 18 | P6G |
| 4 | 413 | 0.64 | 0.78 | 40 | empty |
| 5 | 338 | 0.60 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1009 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1N5R · Crystal structure of the mouse acetylcholinesterase-propidium complex · the same entry in another collection · chain A against A, TM-score 1.00
- P21836 · AlphaFold monomer V2.0 prediction for acetylcholinesterase (P21836) · 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 P21836
- Elsewhere: RCSB PDB 1N5R · PDBe 1N5R · UniProt P21836
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