Research workbench
Cryoem reconstruction of full-length, fully-glycosylated human butyrylcholinesterase tetramer
Analyse Cryoem reconstruction of full-length, fully-glycosylated human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I2T
- Type
- protein
- Length
- 2,252 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholinesterase; Lamellipodin-derived polyproline peptide
- EC
- 3.1.1.8
- UniProt
- P06276
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Cholinesterase (EC 3.1.1.8) | protein | 562 | 38% helix, 16% strand | P06276 |
| A, C | Cholinesterase (EC 3.1.1.8) | protein | 558 | 38% helix, 16% strand | P06276 |
| J | Lamellipodin-derived polyproline peptide | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.77 | 0.78 | 92 | empty |
| 2 | 1084 | 0.77 | 0.79 | 87 | empty |
| 3 | 568 | 0.76 | 0.83 | 45 | empty |
| 4 | 568 | 0.76 | 0.83 | 46 | empty |
| 5 | 503 | 0.75 | 0.83 | 45 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1435 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 1414 Ų buried · 7 hydrogen bonds · protein-protein
- A–J · 352 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 324 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 321 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6I2T · CryoEM reconstruction of full-length, fully-glycosylated human butyrylcholinesterase… · the same entry in another collection · chain J against J, TM-score 1.00
- P06276 · AlphaFold monomer V2.0 prediction for cholinesterase (P06276) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 6I2T · PDBe 6I2T · UniProt P06276
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