MolNFT v1 · #147758 · protein
X-ray structure of the N15'C mutant of glic in complex with bromoform
6EMX · Proton-gated ion channel: “X-ray structure of the N15'C mutant of glic in complex with bromoform”. X-ray diffraction, 3 ligands (MBR, NA, CL), 20 pockets (best druggability 0.81). MolNFT v1 #147758 on GenesisL1: 3D structure…
- PDB
- 6EMX
- Type
- protein
- Length
- 1,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proton-gated ion channel
- UniProt
- Q7NDN8
- Ligands
- MBR, NA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proton-gated ion channel | protein | 311 | 36% helix, 34% strand | Q7NDN8 |
Ligands and binding sites
- MBR · Tribromomethane · ligand · 6 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 6 copies · chains A, B, E, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.81 | 0.82 | 63 | NA, MBR |
| 2 | 397 | 0.72 | 0.83 | 48 | empty |
| 3 | 422 | 0.72 | 0.82 | 46 | empty |
| 4 | 364 | 0.72 | 0.83 | 48 | empty |
| 5 | 380 | 0.71 | 0.83 | 47 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2370 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2354 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2342 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 2286 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 2284 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6EMX · X-ray structure of the N15'C mutant of GLIC in complex with bromoform · the same entry in another collection · chain E against E, TM-score 1.00
- Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · chain D 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 Q7NDN8
- Elsewhere: RCSB PDB 6EMX · PDBe 6EMX · UniProt Q7NDN8
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