Research workbench
Crystal structure of glycine binding protein in complex with strychnine
Analyse Crystal structure of glycine binding protein in complex with strychnine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OBG
- Type
- protein
- Length
- 1,038 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- SY9, NAG, NA
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Soluble acetylcholine receptor | protein | 206 | 9% helix, 52% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 208 | 10% helix, 47% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 212 | 10% helix, 47% strand | Q8WSF8 |
Ligands and binding sites
- SY9 · Strychnine · ligand · 5 copies · chains A, B, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, C, D, E
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 31 copies · chains A, E, B, C, D
- ACT · Acetate ion · additive · 9 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.71 | 0.81 | 46 | SY9 |
| 2 | 432 | 0.71 | 0.82 | 45 | SY9 |
| 3 | 536 | 0.70 | 0.80 | 48 | ACT, EDO, SY9 |
| 4 | 490 | 0.70 | 0.80 | 47 | SY9, ACT, EDO |
| 5 | 547 | 0.70 | 0.79 | 46 | SY9, ACT, EDO |
Interfaces
5 interfaces between chains.
- B–C · 1426 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1384 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1349 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1327 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1282 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5OBG · Crystal structure of glycine binding protein in complex with strychnine · 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 5OBG · PDBe 5OBG · UniProt Q8WSF8
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