MolNFT v1 · #172225 · protein
Complex between SMAD2 MH2 domain and peptide from ski corepressor
6ZVQ · Mothers against decapentaplegic homolog 2: “Complex between SMAD2 MH2 domain and peptide from ski corepressor”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.27). MolNFT v1 #172225 on GenesisL1: 3D structure…
- PDB
- 6ZVQ
- Type
- protein
- Length
- 229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog 2; Ski oncogene
- UniProt
- Q15796, P12755
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 2 | protein | 202 | 27% helix, 28% strand | Q15796 |
| B | Ski oncogene | protein | 27 | 63% helix, 0% strand | P12755 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 8 copies · chains A, B
- TAR · D(-)-tartaric acid · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 923 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6ZVQ · Complex between SMAD2 MH2 domain and peptide from Ski corepressor · the same entry in another collection · chain A against A, TM-score 1.00
- Q15796 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 2 (Q15796) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P12755 · AlphaFold monomer V2.0 prediction for ski oncogene (P12755) · a predicted model of the same protein · chain B against A, TM-score 0.46
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 Q15796
- Every structure of UniProt P12755
- Elsewhere: RCSB PDB 6ZVQ · PDBe 6ZVQ · UniProt Q15796 · UniProt P12755
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