Research workbench
The binding domain of skn-1 in complex with DNA: a new DNA-binding motif
Analyse The binding domain of skn-1 in complex with DNA: a new DNA-binding motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SKN
- Type
- protein + DNA
- Length
- 104 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)- 3'); DNA…
- UniProt
- P34707
- Pockets
- 2 · best druggability 0.46
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*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)- 3') | dna | 15 | — | — |
| B | DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)- 3') | dna | 15 | — | — |
| P | DNA-binding domain of skn-1 | protein | 74 | 73% helix, 0% strand | P34707 |
Ligands and binding sites
- LDA · Lauryl dimethylamine-N-oxide · additive · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.46 | 0.81 | 15 | empty |
| 2 | 134 | 0.44 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 603 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- B–P · 532 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–P · 401 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1SKN · The binding domain of skn-1 in complex with DNA: a new DNA-binding motif · the same entry in another collection · chain A against A, TM-score 1.00
- P34707 · AlphaFold monomer V2.0 prediction for protein skinhead-1 (P34707) · a predicted model of the same protein · chain P against A, TM-score 0.91
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 P34707
- Elsewhere: RCSB PDB 1SKN · PDBe 1SKN · UniProt P34707
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