Research workbench
DNA recognition is mediated by conformational transition and by DNA bending
Analyse DNA recognition is mediated by conformational transition and by DNA bending in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LJM
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RUNX1 transcription factor
- UniProt
- Q01196
- Ligands
- CL
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RUNX1 transcription factor | protein | 114 | 0% helix, 41% strand | Q01196 |
| B | RUNX1 transcription factor | protein | 114 | 0% helix, 39% strand | Q01196 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.62 | 0.83 | 31 | empty |
| 2 | 127 | 0.39 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 667 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1LJM · DNA recognition is mediated by conformational transition and by DNA bending · the same entry in another collection · chain A against A, TM-score 1.00
- Q01196 · AlphaFold monomer V2.0 prediction for runt-related transcription factor 1 (Q01196) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q01196
- Elsewhere: RCSB PDB 1LJM · PDBe 1LJM · UniProt Q01196
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