MolNFT v1 · #186118 · protein
Structure of sarin phosphonylated acetylcholinesterase in complex with 2-((HYDROXYIMINO)METHYL)-1-(5-(4-methyl-3-NITROBENZAMIDO)PENTYL) pyridinium
7R0A: “Structure of sarin phosphonylated acetylcholinesterase in complex with…”. X-ray diffraction, 4 ligands (TOE, I4H, P15), 15 pockets (best druggability 0.71). MolNFT v1 #186118 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7R0A
- Type
- protein
- Length
- 1,072 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
- TOE, I4H, P15, NAG
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholinesterase (EC 3.1.1.7) | protein | 537 | 38% helix, 18% strand | P21836 |
| B | Acetylcholinesterase (EC 3.1.1.7) | protein | 535 | 37% helix, 18% strand | P21836 |
Ligands and binding sites
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · 3 copies · chains A, B
- I4H · ~{N}-ethyl-4-methyl-3-nitro-benzamide · ligand · 2 copies · chains A, B
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.71 | 0.97 | 24 | empty |
| 2 | 155 | 0.67 | 0.87 | 18 | P15 |
| 3 | 179 | 0.67 | 0.86 | 34 | I4H |
| 4 | 191 | 0.58 | 0.81 | 17 | empty |
| 5 | 279 | 0.56 | 0.76 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1010 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 7R0A · Structure of sarin phosphonylated acetylcholinesterase 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 7R0A · PDBe 7R0A · UniProt P21836
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