MolNFT v1 · #163254 · protein
Crystal structure of tetr-Q116A from acinetobacter baumannii aye in complex with minocycline
6RXB · Tetracycline repressor protein class G: “Crystal structure of tetr-Q116A from acinetobacter baumannii aye in complex with minocycline”. X-ray diffraction, 3 ligands (MIY, MG, CL), 11 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6RXB
- Type
- protein
- Length
- 747 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetracycline repressor protein class G
- UniProt
- B0VCI2
- Ligands
- MIY, MG, CL
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tetracycline repressor protein class G | protein | 200 | 68% helix, 0% strand | B0VCI2 |
| D | Tetracycline repressor protein class G | protein | 190 | 67% helix, 0% strand | B0VCI2 |
| A | Tetracycline repressor protein class G | protein | 179 | 74% helix, 0% strand | B0VCI2 |
| C | Tetracycline repressor protein class G | protein | 178 | 72% helix, 0% strand | B0VCI2 |
Ligands and binding sites
- MIY · (4s,4as,5ar,12as)-4,7-bis(dimethylamino)-3,10,12,12A-tetrahydroxy-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · 4 copies · chains B, D, A, C
- MG · Magnesium ion · metal · 4 copies · chains B, A, D, C
- CL · Chloride ion · ion · 2 copies · chains D, C, A
- SIN · Succinic acid · additive · chains D, C
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.81 | 0.86 | 61 | MIY, MG |
| 2 | 583 | 0.77 | 0.83 | 48 | MIY, MG |
| 3 | 386 | 0.76 | 0.85 | 33 | MIY, MG |
| 4 | 414 | 0.71 | 0.82 | 35 | MIY, MG |
| 5 | 183 | 0.53 | 0.79 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–A · 2436 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 2174 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 257 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6RXB · Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE in complex with… · the same entry in another collection · chain B against B, 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 B0VCI2
- Elsewhere: RCSB PDB 6RXB · PDBe 6RXB · UniProt B0VCI2
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