MolNFT v1 · #15001 · protein
Crystal structure of a SMAD4-ski complex
1MR1 · Mothers against decapentaplegic homolog 4: “Crystal structure of a SMAD4-ski complex”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.82). MolNFT v1 #15001 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1MR1
- Type
- protein
- Length
- 581 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog 4; Ski oncogene
- UniProt
- Q13485, P12755
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 4 | protein | 195 | 22% helix, 30% strand | Q13485 |
| B | Mothers against decapentaplegic homolog 4 | protein | 193 | 23% helix, 31% strand | Q13485 |
| C | Ski oncogene | protein | 97 | 30% helix, 21% strand | P12755 |
| D | Ski oncogene | protein | 96 | 26% helix, 22% strand | P12755 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.82 | 0.83 | 97 | empty |
| 2 | 211 | 0.57 | 0.79 | 39 | empty |
| 3 | 84 | 0.49 | 0.83 | 20 | empty |
| 4 | 93 | 0.37 | 0.76 | 19 | empty |
| 5 | 61 | 0.32 | 0.75 | 12 | empty |
Interfaces
6 interfaces between chains.
- B–C · 914 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 885 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 286 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 281 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 121 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1MR1 · Crystal Structure of a Smad4-Ski Complex · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.99
- P12755 · AlphaFold monomer V2.0 prediction for ski oncogene (P12755) · a predicted model of the same protein · chain D against A, TM-score 0.96
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
- Every structure of UniProt P12755
- Elsewhere: RCSB PDB 1MR1 · PDBe 1MR1 · UniProt Q13485 · UniProt P12755
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