MolNFT v1 · #46028 · protein
How an in vitro selected peptide mimics the antibiotic tetracycline to induce tet repressor
2NS8 · Tetracycline repressor protein: “How an in vitro selected peptide mimics the antibiotic tetracycline to induce tet repressor”. X-ray diffraction, 1 ligand (ACE), 12 pockets (best druggability 0.70). MolNFT v1 #46028 on GenesisL1: 3D…
- PDB
- 2NS8
- Type
- protein
- Length
- 858 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetracycline repressor protein; 16 residue peptide tip (transcription inducing peptide)
- UniProt
- P04483, P0ACT4
- Ligands
- ACE
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 7 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetracycline repressor protein | protein | 200 | 72% helix, 0% strand | P04483, P0ACT4 |
| B | Tetracycline repressor protein | protein | 204 | 74% helix, 0% strand | P04483, P0ACT4 |
| C | Tetracycline repressor protein | protein | 206 | 69% helix, 0% strand | P04483, P0ACT4 |
| D | Tetracycline repressor protein | protein | 198 | 76% helix, 0% strand | P04483, P0ACT4 |
| H, F | 16 residue peptide tip (transcription inducing peptide) | protein | 12 | 0% helix, 0% strand | — |
| E, G | 16 residue peptide tip (transcription inducing peptide) | protein | 11 | 36% helix, 0% strand | — |
| Z | 16 residue peptide tip (transcription inducing peptide) | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, H, B, E, C, F, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.70 | 0.97 | 18 | empty |
| 2 | 471 | 0.64 | 0.77 | 61 | empty |
| 3 | 111 | 0.63 | 0.88 | 19 | empty |
| 4 | 122 | 0.61 | 0.86 | 21 | ACE |
| 5 | 234 | 0.59 | 0.80 | 31 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2901 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2732 Ų buried · 28 hydrogen bonds · protein-protein
- B–H · 714 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 685 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 683 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2NS8 · How an in vitro selected peptide mimics the antibiotic tetracycline to induce TET… · the same entry in another collection · chain Z against Z, TM-score 1.00
- P04483 · AlphaFold monomer V2.0 prediction for tetracycline repressor protein class B from… · a predicted model of the same protein · chain D against A, TM-score 0.97
- P0ACT4 · AlphaFold monomer V2.0 prediction for tetracycline repressor protein class D (P0ACT4) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P04483
- Every structure of UniProt P0ACT4
- Elsewhere: RCSB PDB 2NS8 · PDBe 2NS8 · UniProt P04483 · UniProt P0ACT4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.