Research workbench
Crystal structure of the transcriptional regulator TM1030 with 24BP DNA oligonucleotide
Analyse Crystal structure of the transcriptional regulator TM1030 with 24BP DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I6Z
- Type
- protein + DNA
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, tetr family; DNA oligonucleotide
- UniProt
- Q9X0C0
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 82% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcriptional regulator, tetr family | protein | 200 | 82% helix, 1% strand | Q9X0C0 |
| C | DNA oligonucleotide | dna | 12 | — | — |
| D | DNA oligonucleotide | dna | 12 | — | — |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.80 | 0.85 | 52 | empty |
| 2 | 415 | 0.77 | 0.86 | 37 | empty |
| 3 | 186 | 0.63 | 0.84 | 42 | empty |
| 4 | 347 | 0.52 | 0.73 | 28 | empty |
| 5 | 70 | 0.43 | 0.81 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1284 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 518 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- B–C · 310 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–D · 298 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–C · 79 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4I6Z · Crystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide · 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 Q9X0C0
- Elsewhere: RCSB PDB 4I6Z · PDBe 4I6Z · UniProt Q9X0C0
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