Research workbench
Toxin-antitoxin complex from streptococcus pneumoniae
Analyse Toxin-antitoxin complex from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YRZ
- Type
- protein
- Length
- 413 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hicb; Hica
- UniProt
- A0A0H2URC7, A0A0H2URA5
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hicb | protein | 150 | 34% helix, 19% strand | A0A0H2URC7 |
| B, D | Hica | protein | 58 | 34% helix, 24% strand | A0A0H2URA5 |
| C | Hicb | protein | 147 | 35% helix, 17% strand | A0A0H2URC7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.66 | 0.80 | 29 | empty |
| 2 | 108 | 0.50 | 0.81 | 21 | empty |
| 3 | 104 | 0.47 | 0.80 | 20 | empty |
| 4 | 116 | 0.40 | 0.75 | 14 | empty |
| 5 | 63 | 0.30 | 0.75 | 10 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1241 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1175 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5YRZ · Toxin-Antitoxin complex from Streptococcus pneumoniae · the same entry in another collection · chain A against A, 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 A0A0H2URC7
- Every structure of UniProt A0A0H2URA5
- Elsewhere: RCSB PDB 5YRZ · PDBe 5YRZ · UniProt A0A0H2URC7 · UniProt A0A0H2URA5
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