MolNFT v1 · #162708 · protein
TETR(D) N82A mutant in complex with doxycycline and magnesium
6RGX · Tetracycline repressor protein class D: “TETR(D) N82A mutant in complex with doxycycline and magnesium”. X-ray diffraction, 3 ligands (DXT, MG, CL), 5 pockets (best druggability 0.83). MolNFT v1 #162708 on GenesisL1: 3D structure…
- PDB
- 6RGX
- Type
- protein
- Length
- 404 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetracycline repressor protein class D
- UniProt
- P0ACT4
- Ligands
- DXT, MG, CL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetracycline repressor protein class D | protein | 207 | 74% helix, 0% strand | P0ACT4 |
| B | Tetracycline repressor protein class D | protein | 197 | 74% helix, 0% strand | P0ACT4 |
Ligands and binding sites
- DXT · (4s,4ar,5s,5ar,6r,12as)-4-(dimethylamino)-3,5,10,12,12A-pentahydroxy-6-methyl-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 10 copies · chains A, B
- 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.83 | 0.91 | 49 | DXT, MG |
| 2 | 734 | 0.80 | 0.84 | 50 | PG4 |
| 3 | 240 | 0.56 | 0.78 | 35 | empty |
| 4 | 246 | 0.53 | 0.77 | 34 | empty |
| 5 | 51 | 0.32 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2635 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6RGX · TETR(D) N82A mutant in complex with doxycycline 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 P0ACT4
- Elsewhere: RCSB PDB 6RGX · PDBe 6RGX · UniProt P0ACT4
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