Research workbench
Crystal structure of fischerella transcription factor hetr complexed with 21MER DNA target
Analyse Crystal structure of fischerella transcription factor hetr complexed with 21MER… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IZZ
- Type
- protein + DNA
- Length
- 630 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor hetr; DNA (5'- D(*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*…
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcription factor hetr | protein | 294 | 55% helix, 11% strand | — |
| C, D | DNA (5'- D(*GP*TP*GP*AP*GP*GP*GP*GP*TP*TP*AP*AP*AP*CP*CP*CP*CP*TP*CP*AP*C)- 3') | dna | 21 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.85 | 0.86 | 84 | empty |
| 2 | 428 | 0.69 | 0.81 | 38 | SO4 |
| 3 | 375 | 0.65 | 0.80 | 36 | empty |
| 4 | 64 | 0.58 | 0.90 | 21 | empty |
| 5 | 223 | 0.53 | 0.77 | 31 | empty |
Interfaces
6 interfaces between chains.
- A–B · 7368 Ų buried · 103 hydrogen bonds · protein-protein
- C–D · 948 Ų buried · 87 hydrogen bonds · nucleic-nucleic
- A–D · 597 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 569 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 293 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4IZZ · Crystal Structure of Fischerella Transcription Factor HetR complexed with 21mer DNA target · 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
- Elsewhere: RCSB PDB 4IZZ · PDBe 4IZZ
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