Research workbench
Crystal structure of soman-aged human butyrylcholinesterase in complex with methyl 2-(PENTAFLUOROBENZYLOXYIMINO)PYRIDINIUM
Analyse Crystal structure of soman-aged human butyrylcholinesterase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B0P
- 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, MF5, NAG, FUL, CA, NA, K, CL
- 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 | 527 | 37% helix, 17% strand | P06276 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- MF5 · 1-(1-methylpyridin-1-ium-2-yl)-N-[[2,3,4,5,6-pentakis(fluoranyl)phenyl]methoxy]methanimine · 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
- CA · Calcium ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride 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 | 483 | 0.78 | 0.86 | 39 | K, MF5 |
| 2 | 466 | 0.64 | 0.77 | 44 | CL |
| 3 | 100 | 0.37 | 0.75 | 16 | empty |
| 4 | 71 | 0.37 | 0.78 | 20 | CA |
| 5 | 76 | 0.35 | 0.77 | 19 | CA |
Modifications
Observed in the structure: 6 glycan, 3 disulfide, 1 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 4B0P · Crystal structure of soman-aged human butyrylcholinesterase in complex with methyl… · 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 4B0P · PDBe 4B0P · UniProt P06276
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