Research workbench
Crystal structure of the HIGB2 toxin in complex with NB8
Analyse Crystal structure of the HIGB2 toxin in complex with NB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MJE
- Type
- protein
- Length
- 235 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxic translational repressor of toxin-antitoxin stability system; Nanobody 8
- UniProt
- A0A085RXT0
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytotoxic translational repressor of toxin-antitoxin stability system | protein | 111 | 31% helix, 23% strand | A0A085RXT0 |
| B | Nanobody 8 | protein | 124 | 7% helix, 56% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.35 | 0.78 | 17 | empty |
| 2 | 56 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1181 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5MJE · Crystal structure of the HigB2 toxin in complex with Nb8 · 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
- Every structure of UniProt A0A085RXT0
- Elsewhere: RCSB PDB 5MJE · PDBe 5MJE · UniProt A0A085RXT0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.