MolNFT v1 · #126840 · protein + DNA
Crystal structure of SMAD4-MH1 bound to the ggccg site.
5MF0 · MH1 domain of human SMAD4: “Crystal structure of SMAD4-MH1 bound to the ggccg site.”. X-ray diffraction, 2 ligands (ZN, CL), 3 pockets (best druggability 0.48). MolNFT v1 #126840 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5MF0
- Type
- protein + DNA
- Length
- 280 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MH1 domain of human SMAD4; DNA (5'- D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-3'…
- UniProt
- Q13485
- Ligands
- ZN, CL
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MH1 domain of human SMAD4 | protein | 123 | 40% helix, 15% strand | Q13485 |
| B | MH1 domain of human SMAD4 | protein | 125 | 40% helix, 15% strand | Q13485 |
| E, F | DNA (5'- D(P*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*GP*CP*CP*CP*GP*T)-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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.48 | 0.77 | 33 | CL |
| 2 | 103 | 0.44 | 0.79 | 17 | empty |
| 3 | 212 | 0.42 | 0.73 | 18 | empty |
Interfaces
4 interfaces between chains.
- E–F · 759 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–B · 525 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 407 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–F · 178 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 5MF0 · Crystal structure of Smad4-MH1 bound to the GGCCG site. · 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 A against A, TM-score 0.99
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 5MF0 · PDBe 5MF0 · UniProt Q13485
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