MolNFT v1 · #103880 · protein + DNA
Shewanella oneidensis mr-1 toxin antitoxin system hipa, hipb and its operator DNA complex (space group P212121)
4PU3 · Toxin-antitoxin system toxin hipa family: “Shewanella oneidensis mr-1 toxin antitoxin system hipa, hipb and its operator DNA complex (space group…”. X-ray diffraction, 18 pockets (best druggability 0.83). MolNFT v1 #103880 on…
- PDB
- 4PU3
- Type
- protein + DNA
- Length
- 1,043 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toxin-antitoxin system toxin hipa family; Toxin-antitoxin system antidote transcriptional…
- UniProt
- Q8EIX3, Q8EIX4
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Toxin-antitoxin system toxin hipa family | protein | 426 | 38% helix, 17% strand | Q8EIX3 |
| D, C | Toxin-antitoxin system antidote transcriptional repressor xre family | protein | 71 | 56% helix, 6% strand | Q8EIX4 |
| Q | Operator DNA | dna | 25 | — | — |
| P | Operator DNA | dna | 24 | — | — |
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.83 | 0.84 | 87 | empty |
| 2 | 1161 | 0.81 | 0.82 | 73 | empty |
| 3 | 716 | 0.68 | 0.76 | 57 | empty |
| 4 | 556 | 0.65 | 0.77 | 35 | empty |
| 5 | 110 | 0.55 | 0.84 | 21 | empty |
Interfaces
14 interfaces between chains.
- Q–P · 1058 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- D–C · 1005 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 479 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 477 Ų buried · 0 hydrogen bonds · protein-protein
- D–Q · 438 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4PU3 · Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex… · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q8EIX3 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase toxin hipa (Q8EIX3) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q8EIX4 · AlphaFold monomer V2.0 prediction for antitoxin hipb (Q8EIX4) · a predicted model of the same protein · chain D against A, TM-score 0.88
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 Q8EIX3
- Every structure of UniProt Q8EIX4
- Elsewhere: RCSB PDB 4PU3 · PDBe 4PU3 · UniProt Q8EIX3 · UniProt Q8EIX4
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