Research workbench
Crystal structure of the HIGB2 toxin in complex with NB2
Analyse Crystal structure of the HIGB2 toxin in complex with NB2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JA8
- Type
- protein
- Length
- 922 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin higb-2; Nanobody 2
- UniProt
- Q9KMA6
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.66
Structure
x-ray diffraction · 7 distinct chains · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin higb-2 | protein | 105 | 38% helix, 25% strand | Q9KMA6 |
| B | Nanobody 2 | protein | 121 | 5% helix, 47% strand | — |
| C | Toxin higb-2 | protein | 108 | 37% helix, 25% strand | Q9KMA6 |
| D, F | Nanobody 2 | protein | 127 | 5% helix, 46% strand | — |
| E | Toxin higb-2 | protein | 107 | 37% helix, 25% strand | Q9KMA6 |
| G | Toxin higb-2 | protein | 105 | 39% helix, 26% strand | Q9KMA6 |
| H | Nanobody 2 | protein | 122 | 5% helix, 48% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, G
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B, D, F, H
- PDO · 1,3-propandiol · additive · 2 copies · chains C, D, G
- ACT · Acetate ion · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.66 | 0.79 | 45 | EPE |
| 2 | 426 | 0.66 | 0.79 | 42 | EPE |
| 3 | 323 | 0.55 | 0.75 | 33 | empty |
| 4 | 82 | 0.55 | 0.85 | 19 | empty |
| 5 | 123 | 0.54 | 0.81 | 22 | ACT |
Interfaces
14 interfaces between chains.
- A–B · 1063 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1061 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1057 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1034 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 302 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 Q9KMA6
- Elsewhere: RCSB PDB 5JA8 · PDBe 5JA8 · UniProt Q9KMA6
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