MolNFT v1 · #172244 · protein
Human butyrylcholinesterase in complex with ((6-((2E,4E)-5- (BENZO[D][1,3]DIOXOL-5-YL)PENTA-2,4-DIENAMIDO)HEXYL) triphenylphosphonium bromide)
6ZWI: “Human butyrylcholinesterase in complex with ((6-((2E,4E)-5…”. X-ray diffraction, 10 ligands (QRH, LEA, NAG), 5 pockets (best druggability 0.79). MolNFT v1 #172244 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZWI
- 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
- QRH, LEA, NAG, FUC, MAN, GAL, SIA, CL, SO4, BR
- Pockets
- 5 · best druggability 0.79
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 | 527 | 37% helix, 17% strand | P06276 |
Ligands and binding sites
- QRH · (2~{E},4~{E})-5-(1,3-benzodioxol-5-yl)-~{N}-[6-(triphenyl-$l^{5}-phosphanyl)hexyl]penta-2,4-dienamide · ligand · chains A
- LEA · Pentanoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- BR · Bromide ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 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 | 556 | 0.79 | 0.85 | 47 | QRH, LEA |
| 2 | 519 | 0.66 | 0.77 | 46 | BR |
| 3 | 65 | 0.43 | 0.81 | 13 | empty |
| 4 | 130 | 0.41 | 0.75 | 26 | empty |
| 5 | 84 | 0.36 | 0.76 | 18 | SO4 |
Modifications
Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZWI · Human butyrylcholinesterase in complex with ((6-((2E,4E)-5-(benzo[d][1,3]dioxol-5-yl)penta… · 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 6ZWI · PDBe 6ZWI · UniProt P06276
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