MolNFT v1 · #175084 · protein
Cryo-EM strucutre of human acid-sensing ion channel 1A in complex with snake toxin MAMBALGIN1 at pH 8.0
7CFT: “Cryo-EM strucutre of human acid-sensing ion channel 1A in complex with snake toxin MAMBALGIN1 at pH 8.0”. Electron microscopy, 1 ligand (NAG), 16 pockets (best druggability 0.86). MolNFT v1 #175084 on GenesisL1: 3D structure…
- PDB
- 7CFT
- Type
- protein
- Length
- 1,425 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid-sensing ion channel 1; Mambalgin-1
- UniProt
- P78348, P0DKR6
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 25% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acid-sensing ion channel 1 | protein | 418 | 28% helix, 18% strand | P78348 |
| D, E, F | Mambalgin-1 | protein | 57 | 0% helix, 14% strand | P0DKR6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.86 | 0.91 | 100 | empty |
| 2 | 1125 | 0.82 | 0.83 | 106 | empty |
| 3 | 1163 | 0.82 | 0.83 | 102 | empty |
| 4 | 402 | 0.82 | 0.90 | 66 | empty |
| 5 | 1177 | 0.81 | 0.82 | 104 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2189 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2173 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2164 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 864 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 857 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7CFT · Cryo-EM strucutre of human acid-sensing ion channel 1a in complex with snake toxin… · the same entry in another collection · chain F against F, TM-score 1.00
- P78348 · AlphaFold monomer V2.0 prediction for acid-sensing ion channel 1 (P78348) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P0DKR6 · AlphaFold monomer V2.0 prediction for mambalgin-1 (P0DKR6) · a predicted model of the same protein · chain F against A, TM-score 0.74
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 P78348
- Every structure of UniProt P0DKR6
- Elsewhere: RCSB PDB 7CFT · PDBe 7CFT · UniProt P78348 · UniProt P0DKR6
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