Research workbench
Crystal structure of fischerella transcription factor hetr complexed with 29MER DNA target
Analyse Crystal structure of fischerella transcription factor hetr complexed with 29MER… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J01
- Type
- protein + DNA
- Length
- 1,292 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor hetr; DNA (29-mer)
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Transcription factor hetr | protein | 294 | 53% helix, 5% strand | — |
| C, D, G, H | DNA (29-mer) | dna | 29 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.85 | 0.85 | 99 | empty |
| 2 | 641 | 0.82 | 0.86 | 55 | empty |
| 3 | 356 | 0.79 | 0.88 | 51 | empty |
| 4 | 400 | 0.79 | 0.88 | 49 | empty |
| 5 | 496 | 0.77 | 0.85 | 50 | SO4 |
Interfaces
15 interfaces between chains.
- E–F · 7025 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 6869 Ų buried · 78 hydrogen bonds · protein-protein
- G–H · 1273 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- C–D · 1272 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- A–E · 1055 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4J01 · Crystal Structure of Fischerella Transcription Factor HetR complexed with 29mer DNA target · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 4J01 · PDBe 4J01
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