Research workbench
Crystal structure of tetr triple mutant (H64K, S135L, S138I) in complex with 4-ddma-atc
Analyse Crystal structure of tetr triple mutant (H64K, S135L, S138I) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FK7
- Type
- protein
- Length
- 397 residues
- Chains
- 2
- 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
- 4DM, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetracycline repressor protein class B from transposon TN10, tetracycline repressor protein class D | protein | 200 | 73% helix, 0% strand | P04483, P0ACT4 |
| B | Tetracycline repressor protein class B from transposon TN10, tetracycline repressor protein class D | protein | 197 | 73% helix, 0% strand | P04483, P0ACT4 |
Ligands and binding sites
- 4DM · (4aS,12aS)-3,10,11,12a-tetrahydroxy-6-methyl-1,12-dioxo-1,4,4a,5,12,12a-hexahydrotetracene-2-carboxamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.79 | 0.85 | 69 | MG, 4DM |
| 2 | 539 | 0.77 | 0.84 | 58 | MG, 4DM |
| 3 | 90 | 0.61 | 0.89 | 24 | empty |
| 4 | 162 | 0.48 | 0.77 | 20 | empty |
| 5 | 157 | 0.45 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3032 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3FK7 · Crystal structure of TetR triple mutant (H64K, S135L, S138I) in complex with 4-ddma-atc · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.97
- P04483 · AlphaFold monomer V2.0 prediction for tetracycline repressor protein class B from… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 3FK7 · PDBe 3FK7 · UniProt P04483 · UniProt P0ACT4
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