MolNFT v1 · #172810 · protein
Crystal structure of mono-ampylated HEPN(R46E) toxin in complex with mnt antitoxin
7AE9 · Hepn toxin: “Crystal structure of mono-ampylated HEPN(R46E) toxin in complex with mnt antitoxin”. X-ray diffraction, 1 ligand (2DA), 7 pockets (best druggability 0.84). MolNFT v1 #172810 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7AE9
- Type
- protein
- Length
- 1,130 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepn toxin; Mnt antitoxin
- UniProt
- A0A0B0QJR1, A0A0B0QJN8
- Ligands
- 2DA
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 69% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepn toxin | protein | 141 | 79% helix, 0% strand | A0A0B0QJR1 |
| B | Hepn toxin | protein | 137 | 79% helix, 0% strand | A0A0B0QJR1 |
| C | Hepn toxin | protein | 144 | 77% helix, 0% strand | A0A0B0QJR1 |
| D | Hepn toxin | protein | 142 | 78% helix, 0% strand | A0A0B0QJR1 |
| E | Mnt antitoxin | protein | 144 | 60% helix, 17% strand | A0A0B0QJN8 |
| F | Mnt antitoxin | protein | 139 | 60% helix, 17% strand | A0A0B0QJN8 |
| G | Mnt antitoxin | protein | 147 | 60% helix, 16% strand | A0A0B0QJN8 |
| H | Mnt antitoxin | protein | 136 | 57% helix, 18% strand | A0A0B0QJN8 |
Ligands and binding sites
- 2DA · 2',3'-dideoxyadenosine-5'-monophosphate · ligand · 3 copies · chains A, B, F, E, C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.84 | 0.87 | 103 | 2DA |
| 2 | 1008 | 0.82 | 0.83 | 86 | 2DA |
| 3 | 1188 | 0.78 | 0.80 | 94 | 2DA |
| 4 | 511 | 0.76 | 0.84 | 66 | empty |
| 5 | 296 | 0.54 | 0.75 | 40 | empty |
Interfaces
11 interfaces between chains.
- C–G · 1146 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 888 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 881 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 857 Ų buried · 10 hydrogen bonds · protein-protein
- D–H · 832 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7AE9 · Crystal structure of mono-AMPylated HEPN(R46E) toxin in complex with MNT antitoxin · 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 A0A0B0QJR1
- Every structure of UniProt A0A0B0QJN8
- Elsewhere: RCSB PDB 7AE9 · PDBe 7AE9 · UniProt A0A0B0QJR1 · UniProt A0A0B0QJN8
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