MolNFT v2 · #113332 · protein
Crystal structure of a dual topology fluoride ion channel.
5A40 · Putative fluoride ion transporter crcb: “Crystal structure of a dual topology fluoride ion channel.”. X-ray diffraction at 3.6, 1 ligand (HG), 8 pockets (best druggability 0.68). MolNFT v2 #113332 on GenesisL1: 3D structure, binding…
- PDB
- 5A40
- Type
- protein
- Length
- 858 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- BORDETELLA PERTUSSIS; HOMO SAPIENS
- Molecule
- Putative fluoride ion transporter crcb; Monobodies
- UniProt
- Q7VYU0
- Ligands
- HG
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · resolution 3.6 · 4 distinct chains · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative fluoride ion transporter crcb | protein | 127 | 82% helix, 2% strand | Q7VYU0 |
| B, D | Putative fluoride ion transporter crcb | protein | 124 | 84% helix, 2% strand | Q7VYU0 |
| E, H | Monobodies | protein | 90 | 3% helix, 51% strand | — |
| F, G | Monobodies | protein | 88 | 3% helix, 52% strand | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 4 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.68 | 0.91 | 23 | empty |
| 2 | 132 | 0.68 | 0.89 | 23 | empty |
| 3 | 109 | 0.67 | 0.90 | 20 | empty |
| 4 | 177 | 0.66 | 0.85 | 29 | empty |
| 5 | 200 | 0.56 | 0.79 | 32 | HG |
Interfaces
11 interfaces between chains.
- C–D · 1697 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1694 Ų buried · 29 hydrogen bonds · protein-protein
- D–H · 657 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 653 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 612 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5A40 · Crystal structure of a dual topology fluoride ion channel. · the same entry in another collection · chain H against H, 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 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 Q7VYU0
- Elsewhere: RCSB PDB 5A40 · PDBe 5A40 · UniProt Q7VYU0
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