Research workbench
Crystal structure of a mutant binding protein (5HTBP-achbp) in complex with serotonin (5-hydroxytryptamine)
Analyse Crystal structure of a mutant binding protein (5HTBP-achbp) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YMD
- Type
- protein
- Length
- 2,111 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- SRO, PO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, I, J | Soluble acetylcholine receptor | protein | 212 | 8% helix, 49% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 210 | 9% helix, 52% strand | Q8WSF8 |
| H | Soluble acetylcholine receptor | protein | 205 | 9% helix, 50% strand | Q8WSF8 |
Ligands and binding sites
- SRO · Serotonin · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D, H, I, E, F, G, J
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 | 71 | 0.70 | 0.95 | 21 | SRO |
| 2 | 62 | 0.69 | 0.96 | 18 | SRO |
| 3 | 66 | 0.68 | 0.94 | 20 | SRO |
| 4 | 58 | 0.67 | 0.95 | 18 | SRO |
| 5 | 217 | 0.65 | 0.84 | 43 | SRO, PO4 |
Interfaces
20 interfaces between chains.
- F–G · 1498 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1496 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1490 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1488 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1484 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 2YMD · Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with serotonin… · the same entry in another collection · chain D against D, 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 2YMD · PDBe 2YMD · UniProt Q8WSF8
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