MolNFT v1 · #119056 · protein
TETR(D) N82A mutant in complex with anhydrotetracycline and magnesium
5FKK · Tetracycline repressor, class D: “TETR(D) N82A mutant in complex with anhydrotetracycline and magnesium”. X-ray diffraction, 4 ligands (TDC, MG, CL), 6 pockets (best druggability 0.82). MolNFT v1 #119056 on GenesisL1: 3D structure…
- PDB
- 5FKK
- Type
- protein
- Length
- 399 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetracycline repressor, class D
- UniProt
- C6G9U5
- Ligands
- TDC, MG, CL, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetracycline repressor, class D | protein | 203 | 75% helix, 0% strand | C6G9U5 |
| B | Tetracycline repressor, class D | protein | 196 | 74% helix, 0% strand | C6G9U5 |
Ligands and binding sites
- TDC · 5A,6-anhydrotetracycline · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.82 | 0.90 | 53 | TDC, MG |
| 2 | 538 | 0.81 | 0.87 | 50 | PG4 |
| 3 | 240 | 0.53 | 0.77 | 36 | empty |
| 4 | 145 | 0.41 | 0.74 | 23 | empty |
| 5 | 52 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2669 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5FKK · TetR(D) N82A mutant in complex with anhydrotetracycline and magnesium · the same entry in another collection · chain A against A, TM-score 1.00
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 C6G9U5
- Elsewhere: RCSB PDB 5FKK · PDBe 5FKK · UniProt C6G9U5
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