MolNFT v1 · #148854 · protein + DNA
Antitoxin graa in complex with its operator
6FIX · Xre family transcriptional regulator: “Antitoxin graa in complex with its operator”. X-ray diffraction, 9 pockets (best druggability 0.79). MolNFT v1 #148854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FIX
- Type
- protein + DNA
- Length
- 441 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xre family transcriptional regulator; DNA (30-mer)
- UniProt
- A0A179R2V1
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Xre family transcriptional regulator | protein | 95 | 66% helix, 0% strand | A0A179R2V1 |
| B | Xre family transcriptional regulator | protein | 99 | 61% helix, 0% strand | A0A179R2V1 |
| C | DNA (30-mer) | dna | 30 | — | — |
| E | Xre family transcriptional regulator | protein | 92 | 65% helix, 0% strand | A0A179R2V1 |
| F | DNA (30-mer) | dna | 30 | — | — |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.79 | 0.81 | 78 | empty |
| 2 | 351 | 0.75 | 0.86 | 47 | empty |
| 3 | 651 | 0.70 | 0.78 | 43 | empty |
| 4 | 160 | 0.69 | 0.88 | 28 | empty |
| 5 | 182 | 0.66 | 0.85 | 29 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1346 Ų buried · 113 hydrogen bonds · nucleic-nucleic
- A–B · 1251 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1143 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 330 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 312 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6FIX · antitoxin GraA in complex with its operator · 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 A0A179R2V1
- Elsewhere: RCSB PDB 6FIX · PDBe 6FIX · UniProt A0A179R2V1
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