MolNFT v1 · #152451 · protein
Crystal structure of the makes caterpillars floppy (mcf)-like effector of vibrio vulnificus MO6-24/O
6II0 · Putative rtx-toxin: “Crystal structure of the makes caterpillars floppy (mcf)-like effector of vibrio vulnificus MO6-24/O”. X-ray diffraction, 19 pockets (best druggability 0.86). MolNFT v1 #152451 on GenesisL1: 3D structure…
- PDB
- 6II0
- Type
- protein
- Length
- 1,249 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative rtx-toxin
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative rtx-toxin | protein | 328 | 51% helix, 15% strand | — |
| B | Putative rtx-toxin | protein | 329 | 50% helix, 15% strand | — |
| C, D | Putative rtx-toxin | protein | 296 | 48% helix, 16% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.86 | 0.87 | 110 | empty |
| 2 | 1185 | 0.82 | 0.83 | 119 | GOL |
| 3 | 382 | 0.65 | 0.79 | 35 | empty |
| 4 | 477 | 0.65 | 0.77 | 55 | empty |
| 5 | 476 | 0.64 | 0.77 | 54 | empty |
Interfaces
5 interfaces between chains.
- B–D · 3914 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 3889 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 1482 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 336 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 330 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 6II0 · Crystal structure of the Makes Caterpillars Floppy (MCF)-Like effector of Vibrio… · 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 6II0 · PDBe 6II0
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