Research workbench
Crystal structure of the highly open channel-stabilized mutant C27S + K33C + I9'A + N21'C of glic under reducing conditions.
Analyse Crystal structure of the highly open channel-stabilized mutant C27S + K33C +… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V6N
- 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
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D, E | Proton-gated ion channel | protein | 310 | 35% helix, 35% strand | Q7NDN8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C, A, B, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, E, C, B, D
- LMT · Dodecyl-beta-D-maltoside · additive · 5 copies · chains C, B, D, A, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.81 | 0.81 | 81 | LMT, NA |
| 2 | 515 | 0.76 | 0.84 | 61 | empty |
| 3 | 516 | 0.74 | 0.82 | 61 | empty |
| 4 | 496 | 0.74 | 0.82 | 54 | empty |
| 5 | 87 | 0.74 | 0.96 | 20 | empty |
Interfaces
5 interfaces between chains.
- D–E · 2246 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2185 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 2177 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2146 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 2128 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5V6N · Crystal Structure of the highly open channel-stabilized mutant C27S + K33C + I9'A + N21'C… · 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 C 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 5V6N · PDBe 5V6N · UniProt Q7NDN8
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