MolNFT v1 · #54490 · protein
X-ray structure of human butyrylcholinesterase inhibited by pure enantiomer vx-(R)
2XQJ: “X-ray structure of human butyrylcholinesterase inhibited by pure enantiomer vx-(R)”. X-ray diffraction, 10 ligands (GLY, VX, NAG), 5 pockets (best druggability 0.78). MolNFT v1 #54490 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2XQJ
- Type
- protein
- Length
- 527 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholinesterase
- EC
- 3.1.1.8
- UniProt
- P06276
- Ligands
- GLY, VX, NAG, FUL, NA, CA, K, MG, SO4, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholinesterase (EC 3.1.1.8) | protein | 527 | 38% helix, 17% strand | P06276 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- VX · O-ethylmethylphosphonic acid ester group · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.78 | 0.85 | 47 | VX, NA, MG |
| 2 | 566 | 0.67 | 0.77 | 44 | CA |
| 3 | 66 | 0.39 | 0.79 | 18 | NA |
| 4 | 96 | 0.35 | 0.74 | 17 | empty |
| 5 | 59 | 0.32 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 6 glycan, 3 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 2XQJ · X-ray Structure of human butyrylcholinesterase inhibited by pure enantiomer VX-(R) · the same entry in another collection · chain A against A, TM-score 1.00
- P06276 · AlphaFold monomer V2.0 prediction for cholinesterase (P06276) · 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 P06276
- Elsewhere: RCSB PDB 2XQJ · PDBe 2XQJ · UniProt P06276
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