MolNFT v1 · #103881 · protein + DNA
Shewanella oneidensis mr-1 toxin antitoxin system hipa, hipb and its operator DNA complex (space group P21)
4PU4 · Toxin-antitoxin system toxin hipa family: “Shewanella oneidensis mr-1 toxin antitoxin system hipa, hipb and its operator DNA complex (space group P21)”. X-ray diffraction, 16 pockets (best druggability 0.82). MolNFT v1 #103881 on…
- PDB
- 4PU4
- Type
- protein + DNA
- Length
- 1,034 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
- 16 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toxin-antitoxin system toxin hipa family | protein | 420 | 39% helix, 19% strand | Q8EIX3 |
| B | Toxin-antitoxin system toxin hipa family | protein | 419 | 37% helix, 19% strand | Q8EIX3 |
| D | Toxin-antitoxin system antidote transcriptional repressor xre family | protein | 78 | 55% helix, 4% strand | Q8EIX4 |
| Q | Operator DNA | dna | 25 | — | — |
| C | Toxin-antitoxin system antidote transcriptional repressor xre family | protein | 68 | 59% helix, 4% strand | Q8EIX4 |
| P | Operator DNA | dna | 24 | — | — |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.82 | 0.83 | 92 | empty |
| 2 | 1134 | 0.82 | 0.83 | 101 | empty |
| 3 | 857 | 0.72 | 0.77 | 65 | empty |
| 4 | 777 | 0.69 | 0.76 | 58 | empty |
| 5 | 123 | 0.53 | 0.82 | 22 | empty |
Interfaces
13 interfaces between chains.
- Q–P · 1090 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- D–C · 1025 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 497 Ų buried · 3 hydrogen bonds · protein-protein
- C–P · 442 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4PU4 · Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex… · the same entry in another collection · chain P against P, 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 B against A, TM-score 0.98
- Q8EIX4 · AlphaFold monomer V2.0 prediction for antitoxin hipb (Q8EIX4) · a predicted model of the same protein · chain C against A, TM-score 0.90
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 4PU4 · PDBe 4PU4 · UniProt Q8EIX3 · UniProt Q8EIX4
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