Research workbench
Crystal structure of the DNA-binding domain of oct-1 bound to DNA as a dimer
Analyse Crystal structure of the DNA-binding domain of oct-1 bound to DNA as a dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HF0
- Type
- protein + DNA
- Length
- 300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Octamer-binding transcription factor 1; DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP*…
- UniProt
- P14859
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Octamer-binding transcription factor 1 | protein | 128 | 72% helix, 0% strand | P14859 |
| M | DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3' | dna | 22 | — | — |
| N | DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3' | dna | 22 | — | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.70 | 0.80 | 45 | empty |
| 2 | 291 | 0.60 | 0.79 | 35 | empty |
| 3 | 194 | 0.50 | 0.77 | 20 | empty |
| 4 | 89 | 0.47 | 0.81 | 20 | empty |
| 5 | 106 | 0.42 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- M–N · 981 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- A–N · 893 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–M · 858 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–N · 834 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–M · 819 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 1HF0 · Crystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer · the same entry in another collection · chain A against A, TM-score 1.00
- P14859 · AlphaFold monomer V2.0 prediction for pou domain, class 2, transcription factor 1 (P14859) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P14859
- Elsewhere: RCSB PDB 1HF0 · PDBe 1HF0 · UniProt P14859
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