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Structure of recombinant human butyrylcholinesterase in complex with a fluorescent coumarin-based probe
Analyse Structure of recombinant human butyrylcholinesterase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R6V
- Type
- protein
- Length
- 526 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
- JU5, NAG, FUC, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cholinesterase (EC 3.1.1.8) | protein | 526 | 37% helix, 17% strand | P06276 |
Ligands and binding sites
- JU5 · ~{N}-[[(3~{S})-1-[[2-[7-(diethylamino)-2-oxidanylidene-chromen-3-yl]-1,3-thiazol-4-yl]methyl]piperidin-3-yl]methyl]-~{N}-[2-(dimethylamino)ethyl]naphthalene-2-carboxamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
- SO4 · Sulfate ion · ion · 4 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 | 536 | 0.78 | 0.85 | 45 | JU5 |
| 2 | 479 | 0.66 | 0.77 | 47 | SO4 |
| 3 | 58 | 0.38 | 0.80 | 18 | empty |
| 4 | 68 | 0.33 | 0.76 | 18 | SO4 |
| 5 | 59 | 0.29 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6R6V · Structure of recombinant human butyrylcholinesterase in complex with a fluorescent… · 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 6R6V · PDBe 6R6V · UniProt P06276
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