Research workbench
Crystal structure of the N-terminal cut domain of SATB1 bound to matrix attachment region DNA
Analyse Crystal structure of the N-terminal cut domain of SATB1 bound to matrix… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O49
- Type
- protein + DNA
- Length
- 108 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein SATB1; DNA (5'- D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3')…
- UniProt
- Q01826
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-binding protein SATB1 | protein | 84 | 76% helix, 0% strand | Q01826 |
| B | DNA (5'- D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3') | dna | 12 | — | — |
| C | DNA (5'- D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3') | dna | 12 | — | — |
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 | 108 | 0.45 | 0.79 | 19 | empty |
| 2 | 145 | 0.42 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 518 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–C · 328 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–B · 277 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2O49 · Crystal Structure of the N-terminal CUT domain of SATB1 Bound to Matrix Attachment Region… · the same entry in another collection · chain A against A, TM-score 1.00
- Q01826 · AlphaFold monomer V2.0 prediction for DNA-binding protein SATB1 (Q01826) · a predicted model of the same protein · chain A 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 Q01826
- Elsewhere: RCSB PDB 2O49 · PDBe 2O49 · UniProt Q01826
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