Research workbench
Co-crystal structure of ac-achbpp in complex with alpha-conotoxin [D11A]LVIA
Analyse Co-crystal structure of ac-achbpp in complex with alpha-conotoxin [D11A]LVIA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M4Z
- Type
- protein
- Length
- 1,115 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor; Alpha-conotoxin lvia
- UniProt
- Q8WSF8, L8BU87
- Ligands
- NH2
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, G, I | Soluble acetylcholine receptor | protein | 207 | 9% helix, 51% strand | Q8WSF8 |
| F, C, E, H, J | Alpha-conotoxin lvia | protein | 16 | 38% helix, 0% strand | L8BU87 |
Ligands and binding sites
- NH2 · Amino group · ion · 5 copies · chains F, G, A, C, B, E, H, I, D, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.61 | 0.76 | 48 | empty |
| 2 | 383 | 0.61 | 0.77 | 44 | empty |
| 3 | 365 | 0.60 | 0.76 | 46 | empty |
| 4 | 381 | 0.59 | 0.76 | 45 | empty |
| 5 | 376 | 0.59 | 0.76 | 45 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1239 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1218 Ų buried · 13 hydrogen bonds · protein-protein
- A–G · 1174 Ų buried · 14 hydrogen bonds · protein-protein
- D–I · 1166 Ų buried · 16 hydrogen bonds · protein-protein
- G–I · 1159 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 6M4Z · Co-crystal structure of Ac-AChBPP in complex with alpha-conotoxin [D11A]LvIA · the same entry in another collection · chain J against J, TM-score 1.00
- L8BU87 · AlphaFold monomer V2.0 prediction for alpha-conotoxin lvia (L8BU87) · a predicted model of the same protein · chain E against A, TM-score 0.65
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
- Every structure of UniProt L8BU87
- Elsewhere: RCSB PDB 6M4Z · PDBe 6M4Z · UniProt Q8WSF8 · UniProt L8BU87
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