Research workbench
Crystal structure of the highly open channel-stabilized mutant G-2'I + I9'A of glic
Analyse Crystal structure of the highly open channel-stabilized mutant G-2'I + I9'A of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V6O
- Type
- protein
- Length
- 1,550 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proton-gated ion channel
- UniProt
- Q7NDN8
- Ligands
- NA, SO4, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, C | Proton-gated ion channel | protein | 310 | 34% helix, 34% strand | Q7NDN8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B, D, E, C
- SO4 · Sulfate ion · ion · 10 copies · chains A, E, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, D, E, C
- LMT · Dodecyl-beta-D-maltoside · additive · 6 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.81 | 0.82 | 71 | LMT, NA |
| 2 | 416 | 0.76 | 0.85 | 56 | empty |
| 3 | 388 | 0.74 | 0.85 | 47 | empty |
| 4 | 392 | 0.74 | 0.84 | 49 | empty |
| 5 | 362 | 0.73 | 0.84 | 49 | SO4 |
Interfaces
7 interfaces between chains.
- D–E · 2226 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 2214 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2172 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 2172 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2163 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5V6O · Crystal Structure of the highly open channel-stabilized mutant G-2'I + I9'A of GLIC · the same entry in another collection · chain C against C, TM-score 1.00
- 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 0.99
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 5V6O · PDBe 5V6O · UniProt Q7NDN8
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