MolNFT v1 · #109544 · protein
Alpha 1 glycine receptor transmembrane structure fused to the extracellular domain of glic
4X5T · Proton-gated ion CHANNEL,GLRA1 PROTEIN,GLRA1 protein: “Alpha 1 glycine receptor transmembrane structure fused to the extracellular domain of glic”. X-ray diffraction, 2 ligands (NI, CL), 20 pockets (best druggability 0.83). MolNFT…
- PDB
- 4X5T
- Type
- protein
- Length
- 1,536 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proton-gated ion CHANNEL,GLRA1 PROTEIN,GLRA1 protein
- UniProt
- Q7NDN8, Q14C71
- Ligands
- NI, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Proton-gated ion CHANNEL,GLRA1 PROTEIN,GLRA1 protein | protein | 308 | 31% helix, 34% strand | Q7NDN8, Q14C71 |
| E | Proton-gated ion CHANNEL,GLRA1 PROTEIN,GLRA1 protein | protein | 304 | 31% helix, 34% strand | Q7NDN8, Q14C71 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 6 copies · chains A, B, C, E
- ACT · Acetate ion · additive · 5 copies · chains A, E, B, C, D
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 | 576 | 0.83 | 0.88 | 78 | empty |
| 2 | 343 | 0.80 | 0.90 | 41 | empty |
| 3 | 297 | 0.78 | 0.90 | 61 | empty |
| 4 | 216 | 0.77 | 0.91 | 32 | empty |
| 5 | 235 | 0.77 | 0.90 | 32 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1945 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1910 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1887 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1876 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1849 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · chain A against A, TM-score 0.98
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
- Every structure of UniProt Q14C71
- Elsewhere: RCSB PDB 4X5T · PDBe 4X5T · UniProt Q7NDN8 · UniProt Q14C71
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