MolNFT v1 · #121522 · protein
Crystal structure of escherichia COLI toxin lsoa in complex with T4 phage antitoxin dmd
5HY3 · MRNA endoribonuclease lsoa: “Crystal structure of escherichia COLI toxin lsoa in complex with T4 phage antitoxin dmd”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #121522 on GenesisL1: 3D structure, binding…
- 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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