Research workbench
Crystal structure of heterohexameric yoeb-yefm complex bound to 26BP- DNA
Analyse Crystal structure of heterohexameric yoeb-yefm complex bound to 26BP- DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L8E
- Type
- protein + DNA
- Length
- 996 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yefm antitoxin; Yoeb toxin; DNA (26-mer)
- UniProt
- Q2G285, Q2G286
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 9 distinct chains · 49% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I, K | Yefm antitoxin | protein | 83 | 55% helix, 23% strand | Q2G285 |
| B | Yefm antitoxin | protein | 54 | 52% helix, 26% strand | Q2G285 |
| D | Yefm antitoxin | protein | 55 | 51% helix, 24% strand | Q2G285 |
| E, F, M, N | Yoeb toxin | protein | 87 | 38% helix, 29% strand | Q2G286 |
| G, O | DNA (26-mer) | dna | 23 | — | — |
| H | DNA (26-mer) | dna | 22 | — | — |
| J | Yefm antitoxin | protein | 59 | 53% helix, 24% strand | Q2G285 |
| L | Yefm antitoxin | protein | 57 | 51% helix, 25% strand | Q2G285 |
| P | DNA (26-mer) | dna | 23 | — | — |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.86 | 0.92 | 44 | empty |
| 2 | 689 | 0.86 | 0.90 | 48 | empty |
| 3 | 735 | 0.75 | 0.80 | 77 | empty |
| 4 | 579 | 0.66 | 0.77 | 73 | empty |
| 5 | 491 | 0.65 | 0.77 | 44 | empty |
Interfaces
58 interfaces between chains.
- K–N · 1735 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 1732 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 1682 Ų buried · 27 hydrogen bonds · protein-protein
- I–M · 1674 Ų buried · 26 hydrogen bonds · protein-protein
- K–L · 1568 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6L8E · Crystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA · the same entry in another collection · chain P against P, 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 Q2G285
- Every structure of UniProt Q2G286
- Elsewhere: RCSB PDB 6L8E · PDBe 6L8E · UniProt Q2G285 · UniProt Q2G286
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