Research workbench
Structure of a dual topology fluoride channel with monobody S8
Analyse Structure of a dual topology fluoride channel with monobody S8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BQO
- Type
- protein
- Length
- 349 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluoride ion transporter crcb; Monobody S8
- UniProt
- Q7VYU0
- Ligands
- NA, F
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluoride ion transporter crcb | protein | 126 | 84% helix, 0% strand | Q7VYU0 |
| B | Fluoride ion transporter crcb | protein | 128 | 80% helix, 3% strand | Q7VYU0 |
| C | Monobody S8 | protein | 95 | 6% helix, 52% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- F · Fluoride ion · ion · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.76 | 0.88 | 35 | empty |
| 2 | 293 | 0.59 | 0.78 | 35 | empty |
| 3 | 155 | 0.51 | 0.79 | 24 | OLC |
| 4 | 75 | 0.39 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1785 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 624 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 387 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BQO · Structure of a dual topology fluoride channel with monobody S8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q7VYU0 · AlphaFold monomer V2.0 prediction for putative fluoride ion transporter crcb (Q7VYU0) · a predicted model of the same protein · chain B 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 Q7VYU0
- Elsewhere: RCSB PDB 6BQO · PDBe 6BQO · UniProt Q7VYU0
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