Research workbench
Crystal structure of fischerella transcription factor hetr complexed with 24MER DNA target
Analyse Crystal structure of fischerella transcription factor hetr complexed with 24MER… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J00
- Type
- protein + DNA
- Length
- 642 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor hetr; DNA (5'- D(*TP*GP*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*…
- Ligands
- MG
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcription factor hetr | protein | 297 | 52% helix, 10% strand | — |
| C, D | DNA (5'- D(*TP*GP*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP* CP*C)-3') | dna | 24 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.84 | 0.85 | 92 | empty |
| 2 | 339 | 0.79 | 0.89 | 41 | empty |
| 3 | 78 | 0.72 | 0.95 | 22 | empty |
| 4 | 298 | 0.65 | 0.81 | 35 | empty |
| 5 | 423 | 0.63 | 0.77 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–B · 7055 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 1026 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- A–D · 522 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 518 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 275 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 4J00 · Crystal Structure of Fischerella Transcription Factor HetR complexed with 24mer DNA target · 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
- Elsewhere: RCSB PDB 4J00 · PDBe 4J00
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