MolNFT v1 · #115266 · protein
X-ray structure of TOXIN/ANTI-toxin complex from mesorhizobium opportunistum
5CEG · Addiction module antidote protein, COPG/ARC/METJ family: “X-ray structure of TOXIN/ANTI-toxin complex from mesorhizobium opportunistum”. X-ray diffraction, 2 ligands (NA, IOD), 9 pockets (best druggability 0.70). MolNFT v1 #115266…
- PDB
- 5CEG
- Type
- protein
- Length
- 374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Addiction module antidote protein, COPG/ARC/METJ family; Plasmid stabilization system
- UniProt
- F7YBW8, F7YBW7
- Ligands
- NA, IOD
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Addiction module antidote protein, COPG/ARC/METJ family | protein | 85 | 68% helix, 1% strand | F7YBW8 |
| B | Plasmid stabilization system | protein | 103 | 38% helix, 27% strand | F7YBW7 |
| C | Addiction module antidote protein, COPG/ARC/METJ family | protein | 85 | 68% helix, 1% strand | F7YBW8 |
| D | Plasmid stabilization system | protein | 101 | 39% helix, 28% strand | F7YBW7 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B, D
- IOD · Iodide ion · ion · 8 copies · chains A, D, B, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.70 | 0.82 | 36 | IOD |
| 2 | 242 | 0.55 | 0.77 | 27 | GOL |
| 3 | 148 | 0.48 | 0.78 | 23 | GOL, IOD |
| 4 | 152 | 0.43 | 0.74 | 23 | GOL |
| 5 | 115 | 0.41 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1735 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1679 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 576 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 227 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CEG · X-ray structure of toxin/anti-toxin complex from Mesorhizobium opportunistum · 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 F7YBW8
- Every structure of UniProt F7YBW7
- Elsewhere: RCSB PDB 5CEG · PDBe 5CEG · UniProt F7YBW8 · UniProt F7YBW7
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