MolNFT v1 · #30690 · protein
Crystal structure of yefm-yoeb complex
2A6Q · Antitoxin yefm: “Crystal structure of yefm-yoeb complex”. X-ray diffraction, 7 pockets (best druggability 0.86). MolNFT v1 #30690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2A6Q
- Type
- protein
- Length
- 456 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin yefm; Toxin yoeb
- UniProt
- P69346, P69348
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Antitoxin yefm | protein | 86 | 55% helix, 19% strand | P69346 |
| B, D | Antitoxin yefm | protein | 58 | 50% helix, 21% strand | P69346 |
| E, F | Toxin yoeb | protein | 84 | 36% helix, 27% strand | P69348 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.86 | 0.93 | 38 | empty |
| 2 | 235 | 0.49 | 0.74 | 27 | empty |
| 3 | 190 | 0.45 | 0.74 | 31 | empty |
| 4 | 67 | 0.42 | 0.81 | 12 | empty |
| 5 | 161 | 0.41 | 0.73 | 26 | empty |
Interfaces
15 interfaces between chains.
- C–F · 1660 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 1618 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1496 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1397 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 539 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2A6Q · Crystal structure of YefM-YoeB complex · the same entry in another collection · chain F against F, TM-score 1.00
- P69348 · AlphaFold monomer V2.0 prediction for toxin yoeb (P69348) · a predicted model of the same protein · chain E against A, TM-score 0.96
- P69346 · AlphaFold monomer V2.0 prediction for antitoxin yefm (P69346) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P69346
- Every structure of UniProt P69348
- Elsewhere: RCSB PDB 2A6Q · PDBe 2A6Q · UniProt P69346 · UniProt P69348
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