Research workbench
Crystal structure of cocaine bound to an ach-binding protein
Analyse Crystal structure of cocaine bound to an ach-binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PGZ
- Type
- protein
- Length
- 1,056 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- COC, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 211 | 12% helix, 49% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 211 | 12% helix, 52% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 211 | 11% helix, 50% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 214 | 13% helix, 49% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 209 | 12% helix, 52% strand | Q8WSF8 |
Ligands and binding sites
- COC · Cocaine · ligand · 2 copies · chains A, B, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- PG4 · Tetraethylene glycol · additive · 3 copies · chains B, C, D, A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.68 | 0.78 | 59 | COC |
| 2 | 612 | 0.68 | 0.77 | 56 | PG4 |
| 3 | 367 | 0.68 | 0.81 | 41 | COC |
| 4 | 593 | 0.67 | 0.77 | 52 | PG4 |
| 5 | 580 | 0.64 | 0.75 | 61 | PG4 |
Interfaces
5 interfaces between chains.
- A–B · 1353 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1341 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1332 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1302 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1276 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2PGZ · Crystal structure of Cocaine bound to an ACh-Binding Protein · the same entry in another collection · 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 Q8WSF8
- Elsewhere: RCSB PDB 2PGZ · PDBe 2PGZ · UniProt Q8WSF8
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