Research workbench
Crystal structure of escherichia COLI toxin lsoa in complex with T4 phage antitoxin dmd
Analyse Crystal structure of escherichia COLI toxin lsoa in complex with T4 phage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HY3
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA endoribonuclease lsoa; Antitoxin dmd
- EC
- 3.1.-.-
- UniProt
- O82881, P39232
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA endoribonuclease lsoa (EC 3.1.-.-) | protein | 252 | 52% helix, 10% strand | O82881 |
| B | Antitoxin dmd | protein | 57 | 26% helix, 51% strand | P39232 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.72 | 0.80 | 59 | empty |
| 2 | 389 | 0.69 | 0.81 | 34 | empty |
| 3 | 79 | 0.52 | 0.84 | 20 | empty |
| 4 | 56 | 0.38 | 0.80 | 14 | empty |
| 5 | 56 | 0.31 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5HY3 · Crystal structure of Escherichia coli toxin LsoA in complex with T4 phage antitoxin Dmd · the same entry in another collection · chain A against A, TM-score 1.00
- O82881 · AlphaFold monomer V2.0 prediction for mRNA endoribonuclease lsoa (O82881) · a predicted model of the same protein · chain A against A, TM-score 0.69
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 O82881
- Every structure of UniProt P39232
- Elsewhere: RCSB PDB 5HY3 · PDBe 5HY3 · UniProt O82881 · UniProt P39232
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