Research workbench
Crystal structure of tetracycline REPRESSOR/OPERATOR complex
Analyse Crystal structure of tetracycline REPRESSOR/OPERATOR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QPI
- Type
- protein + DNA
- Length
- 225 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3'); DNA (5'…
- UniProt
- P0ACT4
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| M | DNA (5'- D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*GP*AP*TP*AP*GP*A)-3') | dna | 15 | — | — |
| N | DNA (5'- D(*TP*CP*TP*AP*TP*CP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3') | dna | 15 | — | — |
| A | Protein (tetracycline repressor) | protein | 195 | 74% helix, 0% strand | P0ACT4 |
Ligands and binding sites
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.69 | 0.80 | 33 | IMD |
Interfaces
3 interfaces between chains.
- M–A · 265 Ų buried · 1 hydrogen bond · protein-nucleic
- N–A · 262 Ų buried · 1 hydrogen bond · protein-nucleic
- M–N · 82 Ų buried · 112 hydrogen bonds · nucleic-nucleic
Compared structures
- 1QPI · Crystal structure of tetracycline REPRESSOR/OPERATOR complex · the same entry in another collection · chain M against M, TM-score 1.00
- 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 0.94
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 P0ACT4
- Elsewhere: RCSB PDB 1QPI · PDBe 1QPI · UniProt P0ACT4
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