Research workbench
Crystal structure of a-achbp in complex with gymnodimine a
Analyse Crystal structure of a-achbp in complex with gymnodimine a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X00
- Type
- protein
- Length
- 1,068 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- GYN
- Pockets
- 19 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 216 | 12% helix, 48% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 215 | 9% helix, 52% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 213 | 11% helix, 45% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 212 | 11% helix, 49% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 212 | 11% helix, 49% strand | Q8WSF8 |
Ligands and binding sites
- GYN · Gymnodimine A · ligand · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.69 | 0.79 | 51 | GYN |
| 2 | 623 | 0.69 | 0.77 | 53 | GYN |
| 3 | 538 | 0.69 | 0.78 | 52 | GYN |
| 4 | 614 | 0.68 | 0.77 | 53 | GYN |
| 5 | 553 | 0.67 | 0.78 | 50 | GYN |
Interfaces
5 interfaces between chains.
- A–B · 1415 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1370 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1360 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1344 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1344 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2X00 · Crystal structure of a-achbp in complex with gymnodimine a · 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 2X00 · PDBe 2X00 · UniProt Q8WSF8
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