Research workbench
Structure of tetracycline repressor in complex with inducer peptide- TIP2
Analyse Structure of tetracycline repressor in complex with inducer peptide- TIP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZQI
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetracycline repressor protein class B from transposon TN10, tetracycline repressor…
- UniProt
- P04483, P0ACT4
- Ligands
- MG
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tetracycline repressor protein class B from transposon TN10, tetracycline repressor protein class D | protein | 201 | 77% helix, 0% strand | P04483, P0ACT4 |
| C, D | Inducer peptide TIP2 | protein | 14 | 43% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.58 | 0.77 | 36 | MG |
| 2 | 267 | 0.56 | 0.78 | 42 | EDO |
| 3 | 78 | 0.56 | 0.87 | 22 | EDO |
| 4 | 225 | 0.54 | 0.78 | 30 | empty |
| 5 | 77 | 0.54 | 0.86 | 24 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 2876 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 767 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 670 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 631 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 587 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ZQI · Structure of Tetracycline repressor in complex with inducer peptide- TIP2 · the same entry in another collection · chain A against A, 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 A 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 A against A, TM-score 0.95
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 3ZQI · PDBe 3ZQI · UniProt P04483 · UniProt P0ACT4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.