Research workbench
Crystal structure of acetylcholinesterase, phosphonylated by sarin and in complex with hi-6
Analyse Crystal structure of acetylcholinesterase, phosphonylated by sarin and in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WHP
- 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
- P21836
- Ligands
- HI6, NAG, CO3
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 531 | 39% helix, 18% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 529 | 39% helix, 19% strand | P21836 |
Ligands and binding sites
- HI6 · 4-(aminocarbonyl)-1-[({2-[(E)-(hydroxyimino)methyl]pyridinium-1-yl}methoxy)methyl]pyridinium · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- CO3 · Carbonate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
- P6G · Hexaethylene glycol · additive · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.80 | 0.94 | 36 | HI6 |
| 2 | 221 | 0.77 | 0.91 | 37 | HI6 |
| 3 | 162 | 0.67 | 0.87 | 19 | P6G |
| 4 | 302 | 0.57 | 0.77 | 32 | empty |
| 5 | 208 | 0.57 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 979 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 2WHP · Crystal structure of acetylcholinesterase, phosphonylated by sarin and in complex with… · 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 2WHP · PDBe 2WHP · UniProt P21836
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