Research workbench
Crystal structure analysis of the SMAD4 active fragment
Analyse Crystal structure analysis of the SMAD4 active fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DD1
- Type
- protein
- Length
- 711 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SMAD4
- UniProt
- Q13485
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SMAD4 | protein | 221 | 24% helix, 29% strand | Q13485 |
| B | SMAD4 | protein | 249 | 24% helix, 27% strand | Q13485 |
| C | SMAD4 | protein | 241 | 26% helix, 28% strand | Q13485 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.86 | 0.87 | 105 | empty |
| 2 | 233 | 0.59 | 0.80 | 42 | empty |
| 3 | 165 | 0.55 | 0.80 | 33 | empty |
| 4 | 72 | 0.52 | 0.86 | 21 | empty |
| 5 | 112 | 0.47 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1041 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 993 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 871 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1DD1 · Crystal structure analysis of the SMAD4 active fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q13485 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 4 (Q13485) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q13485
- Elsewhere: RCSB PDB 1DD1 · PDBe 1DD1 · UniProt Q13485
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