MolNFT v2 · #149445 · protein
Toxin-Antitoxin complex GraTA
6F8S · XRE family transcriptional regulator: “Toxin-Antitoxin complex GraTA”. X-ray diffraction at 2.5, 1 ligand (SO4), 2 pockets (best druggability 0.65). MolNFT v2 #149445 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F8S
- Type
- protein
- Length
- 320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Pseudomonas putida; Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB…
- Molecule
- XRE family transcriptional regulator; Putative Killer protein
- UniProt
- A0A179R2V1, Q88MI5
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.5 · 4 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | XRE family transcriptional regulator | protein | 94 | 71% helix, 0% strand | A0A179R2V1 |
| B | Putative Killer protein | protein | 66 | 32% helix, 32% strand | Q88MI5 |
| C | XRE family transcriptional regulator | protein | 95 | 67% helix, 0% strand | A0A179R2V1 |
| D | Putative Killer protein | protein | 65 | 34% helix, 26% strand | Q88MI5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.65 | 0.75 | 52 | PEG |
| 2 | 66 | 0.36 | 0.77 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1516 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 801 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 773 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6F8S · Toxin-antitoxin complex grata · 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 A0A179R2V1
- Every structure of UniProt Q88MI5
- Elsewhere: RCSB PDB 6F8S · PDBe 6F8S · UniProt A0A179R2V1 · UniProt Q88MI5
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