Research workbench
Crystal structure of the oct-1 pou domain bound to an octamer site: DNA recognition with tethered DNA-binding modules
Analyse Crystal structure of the oct-1 pou domain bound to an octamer site: DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OCT
- Type
- protein + DNA
- Length
- 161 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3'); DNA (5'…
- UniProt
- P14859
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3') | dna | 15 | — | — |
| B | DNA (5'- D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3') | dna | 15 | — | — |
| C | Protein (oct-1 pou domain) | protein | 131 | 73% helix, 0% strand | P14859 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.40 | 0.77 | 14 | empty |
| 2 | 90 | 0.35 | 0.75 | 13 | empty |
| 3 | 83 | 0.33 | 0.75 | 12 | empty |
| 4 | 50 | 0.23 | 0.72 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 892 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 868 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–B · 638 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Compared structures
- 1OCT · Crystal structure of the oct-1 pou domain bound to an octamer site: DNA recognition with… · 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 C against A, TM-score 0.89
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 1OCT · PDBe 1OCT · UniProt P14859
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