Research workbench
Crystal structure of SMAD8_9-MH1 bound to the ggcgc site.
Analyse Crystal structure of SMAD8_9-MH1 bound to the ggcgc site. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FZT
- Type
- protein + DNA
- Length
- 289 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog 9; DNA (5'…
- UniProt
- O15198
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 9 | protein | 131 | 37% helix, 14% strand | O15198 |
| B | Mothers against decapentaplegic homolog 9 | protein | 126 | 39% helix, 14% strand | O15198 |
| C, D | DNA (5'- D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3') | dna | 16 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.64 | 0.76 | 61 | GOL |
| 2 | 150 | 0.38 | 0.72 | 19 | empty |
| 3 | 129 | 0.35 | 0.72 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 752 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–C · 352 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 351 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 161 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 152 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6FZT · Crystal structure of Smad8_9-MH1 bound to the GGCGC site. · the same entry in another collection · chain A against A, TM-score 1.00
- O15198 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 9 (O15198) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 O15198
- Elsewhere: RCSB PDB 6FZT · PDBe 6FZT · UniProt O15198
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