Research workbench
Escherichia COLI rnla-rnlb toxin-antitoxin system.
Analyse Escherichia COLI rnla-rnlb toxin-antitoxin system. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y2P
- Type
- protein
- Length
- 943 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA endoribonuclease toxin ls; Antitoxin rnlb
- EC
- 3.1.-.-
- UniProt
- P52129, P52130
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA endoribonuclease toxin ls (EC 3.1.-.-) | protein | 355 | 40% helix, 20% strand | P52129 |
| B | MRNA endoribonuclease toxin ls (EC 3.1.-.-) | protein | 348 | 41% helix, 19% strand | P52129 |
| C, D | Antitoxin rnlb | protein | 120 | 35% helix, 30% strand | P52130 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.78 | 0.80 | 100 | empty |
| 2 | 517 | 0.71 | 0.80 | 59 | empty |
| 3 | 541 | 0.63 | 0.76 | 47 | empty |
| 4 | 185 | 0.62 | 0.83 | 28 | empty |
| 5 | 93 | 0.38 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3841 Ų buried · 81 hydrogen bonds · protein-protein
- B–D · 917 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 336 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 151 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Y2P · Escherichia coli RnlA-RnlB Toxin-Antitoxin System. · the same entry in another collection · chain A against A, TM-score 1.00
- P52130 · AlphaFold monomer V2.0 prediction for antitoxin rnlb (P52130) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P52129 · AlphaFold monomer V2.0 prediction for mRNA endoribonuclease toxin ls (P52129) · a predicted model of the same protein · chain A against A, TM-score 0.52
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 P52129
- Every structure of UniProt P52130
- Elsewhere: RCSB PDB 6Y2P · PDBe 6Y2P · UniProt P52129 · UniProt P52130
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