MolNFT v1 · #12473 · protein
SMAD1 crystal structure reveals the details of bmp signaling pathway
1KHU: “SMAD1 crystal structure reveals the details of bmp signaling pathway”. X-ray diffraction, 11 pockets (best druggability 0.84). MolNFT v1 #12473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KHU
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SMAD1
- UniProt
- Q15797
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SMAD1 | protein | 198 | 24% helix, 28% strand | Q15797 |
| B, C | SMAD1 | protein | 197 | 28% helix, 30% strand | Q15797 |
| D | SMAD1 | protein | 184 | 27% helix, 30% strand | Q15797 |
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 | 989 | 0.84 | 0.85 | 93 | empty |
| 2 | 236 | 0.61 | 0.81 | 29 | empty |
| 3 | 258 | 0.60 | 0.80 | 30 | empty |
| 4 | 217 | 0.59 | 0.81 | 24 | empty |
| 5 | 53 | 0.44 | 0.84 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1304 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1268 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1207 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 390 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 319 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1KHU · Smad1 crystal structure reveals the details of BMP signaling pathway · the same entry in another collection · chain A against A, TM-score 1.00
- Q15797 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 1 (Q15797) · a predicted model of the same protein · chain D 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 Q15797
- Elsewhere: RCSB PDB 1KHU · PDBe 1KHU · UniProt Q15797
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