MolNFT v1 · #85898 · protein
Crystal structure of fully glycosylated human butyrylcholinesterase
4AQD: “Crystal structure of fully glycosylated human butyrylcholinesterase”. X-ray diffraction, 7 ligands (BAL, GLY, NAG), 10 pockets (best druggability 0.80). MolNFT v1 #85898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AQD
- Type
- protein
- Length
- 1,053 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Butyrylcholinesterase
- EC
- 3.1.1.8
- UniProt
- P06276
- Ligands
- BAL, GLY, NAG, FUL, MAN, UNX, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Butyrylcholinesterase (EC 3.1.1.8) | protein | 527 | 35% helix, 18% strand | P06276 |
| B | Butyrylcholinesterase (EC 3.1.1.8) | protein | 526 | 36% helix, 17% strand | P06276 |
Ligands and binding sites
- BAL · Beta-alanine · ligand · 2 copies · chains A, B
- GLY · Glycine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains B
- UNX · Unknown atom or ion · ion · 10 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.80 | 0.81 | 78 | NAG, EDO, CL, BAL, UNX |
| 2 | 560 | 0.78 | 0.85 | 46 | BAL, EDO, UNX |
| 3 | 371 | 0.60 | 0.76 | 41 | EDO |
| 4 | 353 | 0.59 | 0.76 | 42 | EDO, CL |
| 5 | 149 | 0.44 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 750 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
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 4AQD · PDBe 4AQD · UniProt P06276
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