MolNFT v1 · #184394 · protein + DNA
X-ray structure of interferon regulatory factor 4 DNA binding domain bound to an interferon-stimulated response element
7OOT: “X-ray structure of interferon regulatory factor 4 DNA binding domain bound to an interferon-stimulated…”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.52). MolNFT v1 #184394 on GenesisL1: 3D structure, binding…
- PDB
- 7OOT
- Type
- protein + DNA
- Length
- 262 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon regulatory factor 4; DNA (5'- D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*…
- UniProt
- Q15306
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Interferon regulatory factor 4 | protein | 111 | 37% helix, 15% strand | Q15306 |
| C | DNA (5'- D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*AP*AP*AP*GP*C)-3') | dna | 20 | — | — |
| E | DNA (5'- D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3') | dna | 20 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.52 | 0.76 | 32 | empty |
| 2 | 71 | 0.46 | 0.82 | 18 | empty |
| 3 | 52 | 0.42 | 0.83 | 19 | empty |
| 4 | 128 | 0.41 | 0.76 | 17 | empty |
| 5 | 92 | 0.40 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–E · 868 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–E · 603 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–E · 516 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 437 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 422 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7OOT · X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15306 · AlphaFold monomer V2.0 prediction for interferon regulatory factor 4 (Q15306) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q15306
- Elsewhere: RCSB PDB 7OOT · PDBe 7OOT · UniProt Q15306
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