MolNFT v1 · #123120 · protein
Crystal structure of the HIGBA2 toxin-antitoxin complex
5JAA · Antitoxin IgA-2: “Crystal structure of the HIGBA2 toxin-antitoxin complex”. X-ray diffraction, 3 pockets (best druggability 0.64). MolNFT v1 #123120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JAA
- Type
- protein
- Length
- 407 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin IgA-2; Toxin higb-2
- UniProt
- Q9KMA5, Q9KMA6
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antitoxin IgA-2 | protein | 102 | 60% helix, 4% strand | Q9KMA5 |
| B | Antitoxin IgA-2 | protein | 101 | 59% helix, 5% strand | Q9KMA5 |
| C | Toxin higb-2 | protein | 102 | 40% helix, 25% strand | Q9KMA6 |
| D | Toxin higb-2 | protein | 102 | 38% helix, 28% strand | Q9KMA6 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.64 | 0.80 | 41 | empty |
| 2 | 204 | 0.55 | 0.78 | 22 | empty |
| 3 | 67 | 0.35 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1387 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1382 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1153 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 333 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 304 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 5JAA · Crystal structure of the HigBA2 toxin-antitoxin complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9KMA6 · AlphaFold monomer V2.0 prediction for toxin higb-2 (Q9KMA6) · a predicted model of the same protein · chain D against A, TM-score 0.83
- Q9KMA5 · AlphaFold monomer V2.0 prediction for antitoxin higa-2 (Q9KMA5) · a predicted model of the same protein · chain A against A, TM-score 0.68
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 Q9KMA5
- Every structure of UniProt Q9KMA6
- Elsewhere: RCSB PDB 5JAA · PDBe 5JAA · UniProt Q9KMA5 · UniProt Q9KMA6
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