Research workbench
How an in vitro selected peptide mimics the antibiotic tetracycline to induce tet repressor
Analyse How an in vitro selected peptide mimics the antibiotic tetracycline to induce… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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