MolNFT v1 · #54835 · protein
Structure of human butyrylcholinesterase inhibited by cbdp (12H soak): phosphoserine adduct
2Y1K: “Structure of human butyrylcholinesterase inhibited by cbdp (12H soak): phosphoserine adduct”. X-ray diffraction, 5 ligands (NAG, FUC, NA), 6 pockets (best druggability 0.76). MolNFT v1 #54835 on GenesisL1: 3D structure, binding…
- PDB
- 2Y1K
- Type
- protein
- Length
- 525 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
- NAG, FUC, NA, SO4, CL
- Pockets
- 6 · best druggability 0.76
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 | 525 | 38% helix, 17% strand | P06276 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.76 | 0.84 | 42 | empty |
| 2 | 483 | 0.66 | 0.78 | 45 | SO4 |
| 3 | 81 | 0.39 | 0.77 | 20 | CL |
| 4 | 52 | 0.36 | 0.79 | 14 | empty |
| 5 | 57 | 0.33 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 3 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, phosphorylation).
Compared structures
- 2Y1K · Structure of human butyrylcholinesterase inhibited by cbdp (12H soak): phosphoserine… · 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 2Y1K · PDBe 2Y1K · UniProt P06276
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