MolNFT v1 · #154270 · protein
Structure of mosquito-larvicidal binary toxin receptor, CQM1
6K5P · Binary toxin receptor protein: “Structure of mosquito-larvicidal binary toxin receptor, CQM1”. X-ray diffraction, 4 ligands (CD, MG, CA), 19 pockets (best druggability 0.66). MolNFT v1 #154270 on GenesisL1: 3D structure, binding…
- PDB
- 6K5P
- Type
- protein
- Length
- 2,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Binary toxin receptor protein
- Ligands
- CD, MG, CA, CO
- Pockets
- 19 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Binary toxin receptor protein | protein | 531 | 30% helix, 19% strand | — |
| D | Binary toxin receptor protein | protein | 529 | 31% helix, 19% strand | — |
Ligands and binding sites
- CD · Cadmium ion · metal · 14 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 2 copies · chains C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.66 | 0.84 | 36 | empty |
| 2 | 218 | 0.65 | 0.84 | 29 | empty |
| 3 | 220 | 0.65 | 0.84 | 33 | empty |
| 4 | 698 | 0.65 | 0.75 | 73 | CD |
| 5 | 667 | 0.65 | 0.75 | 75 | CD |
Interfaces
4 interfaces between chains.
- C–D · 1444 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 602 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 576 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6K5P · Structure of mosquito-larvicidal Binary toxin receptor, Cqm1 · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 6K5P · PDBe 6K5P
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