MolNFT v1 · #54491 · protein
X-ray structure of human butyrylcholinesterase inhibited by pure enantiomer vx-(S)
2XQK: “X-ray structure of human butyrylcholinesterase inhibited by pure enantiomer vx-(S)”. X-ray diffraction, 10 ligands (GLY, VX, NAG), 5 pockets (best druggability 0.79). MolNFT v1 #54491 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2XQK
- 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, FUC, CA, NA, K, UNX, SO4, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholinesterase (EC 3.1.1.8) | protein | 527 | 37% helix, 16% 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
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- K · Potassium ion · metal · chains A
- UNX · Unknown atom or ion · ion · 25 copies · 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 | 569 | 0.79 | 0.85 | 47 | VX |
| 2 | 589 | 0.68 | 0.77 | 48 | UNX |
| 3 | 60 | 0.40 | 0.80 | 14 | CA |
| 4 | 97 | 0.35 | 0.74 | 17 | UNX |
| 5 | 68 | 0.33 | 0.76 | 17 | UNX |
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 2XQK · X-ray Structure of human butyrylcholinesterase inhibited by pure enantiomer VX-(S) · 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 2XQK · PDBe 2XQK · UniProt P06276
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