MolNFT v1 · #111086 · protein + DNA
Structure of fl autorepression promoter complex
4YG7 · Antitoxin hipb: “Structure of fl autorepression promoter complex”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #111086 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YG7
- Type
- protein + DNA
- Length
- 1,206 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin hipb; SERINE/THREONINE-protein kinase hipa; DNA (50-mer)
- EC
- 2.7.11.1
- UniProt
- P23873, P23874
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | Antitoxin hipb | protein | 69 | 61% helix, 9% strand | P23873 |
| D | SERINE/THREONINE-protein kinase hipa (EC 2.7.11.1) | protein | 414 | 33% helix, 10% strand | P23874 |
| R | DNA (50-mer) | dna | 50 | — | — |
| T | DNA (50-mer) | dna | 50 | — | — |
| C, G | Antitoxin hipb | protein | 71 | 48% helix, 10% strand | P23873 |
| K | SERINE/THREONINE-protein kinase hipa (EC 2.7.11.1) | protein | 412 | 30% helix, 14% strand | P23874 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.81 | 0.95 | 41 | empty |
| 2 | 83 | 0.75 | 0.97 | 24 | empty |
| 3 | 1130 | 0.75 | 0.78 | 95 | empty |
| 4 | 519 | 0.74 | 0.82 | 72 | empty |
| 5 | 1181 | 0.73 | 0.77 | 88 | empty |
Interfaces
20 interfaces between chains.
- R–T · 2222 Ų buried · 158 hydrogen bonds · nucleic-nucleic
- C–G · 1413 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1364 Ų buried · 23 hydrogen bonds · protein-protein
- D–K · 1057 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 596 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4YG7 · Structure of FL autorepression promoter complex · the same entry in another collection · chain K against K, TM-score 1.00
- P23874 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase toxin hipa (P23874) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P23873 · AlphaFold monomer V2.0 prediction for antitoxin hipb (P23873) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P23873
- Every structure of UniProt P23874
- Elsewhere: RCSB PDB 4YG7 · PDBe 4YG7 · UniProt P23873 · UniProt P23874
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