Research workbench
Mmts-modified Y53C mutant of aplysia achbp in complex with acetylcholine
Analyse Mmts-modified Y53C mutant of aplysia achbp in complex with acetylcholine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XZ5
- Type
- protein
- Length
- 1,035 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- ACH, NAG, PO4, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Soluble acetylcholine receptor | protein | 207 | 7% helix, 50% strand | Q8WSF8 |
Ligands and binding sites
- ACH · Acetylcholine · ligand · 10 copies · chains A, B, E, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D
- PO4 · Phosphate ion · ion · 10 copies · chains A, C, B, E, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B, C, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.71 | 0.81 | 56 | ACH |
| 2 | 451 | 0.71 | 0.81 | 57 | ACH |
| 3 | 449 | 0.71 | 0.81 | 55 | ACH |
| 4 | 411 | 0.70 | 0.82 | 55 | ACH |
| 5 | 433 | 0.70 | 0.81 | 53 | ACH |
Interfaces
5 interfaces between chains.
- C–D · 1430 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1424 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1416 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1406 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1384 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 5 modified (disulfide, methylation).
Compared structures
- 2XZ5 · MMTS-modified Y53C mutant of Aplysia AChBP in complex with acetylcholine · 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 2XZ5 · PDBe 2XZ5 · UniProt Q8WSF8
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