Research workbench
Crystal structure of bacillus subtilis toxin mazf in complex with cognate antitoxin maze
Analyse Crystal structure of bacillus subtilis toxin mazf in complex with cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ME7
- Type
- protein
- Length
- 583 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA interferase endoa; Antitoxin endoai
- EC
- 3.1.-.-
- UniProt
- P96622, P96621
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA interferase endoa (EC 3.1.-.-) | protein | 105 | 23% helix, 32% strand | P96622 |
| B | MRNA interferase endoa (EC 3.1.-.-) | protein | 108 | 19% helix, 40% strand | P96622 |
| C | MRNA interferase endoa (EC 3.1.-.-) | protein | 110 | 19% helix, 37% strand | P96622 |
| D | MRNA interferase endoa (EC 3.1.-.-) | protein | 103 | 20% helix, 40% strand | P96622 |
| E | Antitoxin endoai | protein | 78 | 79% helix, 5% strand | P96621 |
| F | Antitoxin endoai | protein | 79 | 78% helix, 5% strand | P96621 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.59 | 0.81 | 38 | empty |
| 2 | 216 | 0.50 | 0.75 | 40 | empty |
| 3 | 78 | 0.48 | 0.83 | 16 | empty |
| 4 | 69 | 0.31 | 0.74 | 18 | empty |
| 5 | 61 | 0.30 | 0.75 | 16 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1916 Ų buried · 30 hydrogen bonds · protein-protein
- B–E · 903 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 886 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 828 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 815 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 4ME7 · Crystal structure of Bacillus subtilis toxin MazF in complex with cognate antitoxin MazE · the same entry in another collection · chain F against F, TM-score 1.00
- P96622 · AlphaFold monomer V2.0 prediction for endoribonuclease endoa (P96622) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P96621 · AlphaFold monomer V2.0 prediction for antitoxin endoai (P96621) · a predicted model of the same protein · chain E against A, TM-score 0.84
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 P96622
- Every structure of UniProt P96621
- Elsewhere: RCSB PDB 4ME7 · PDBe 4ME7 · UniProt P96622 · UniProt P96621
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