MolNFT v1 · #128300 · protein + DNA
Crystal structure of the placozoa trichoplax adhaerens SMAD4-MH1 bound to the ggcgc site.
5NM9 · Mothers against decapentaplegic homolog: “Crystal structure of the placozoa trichoplax adhaerens SMAD4-MH1 bound to the ggcgc site.”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.48). MolNFT v1 #128300 on…
- PDB
- 5NM9
- Type
- protein + DNA
- Length
- 281 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog; DNA (5'…
- UniProt
- B3S7S5
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog | protein | 122 | 41% helix, 15% strand | B3S7S5 |
| B | Mothers against decapentaplegic homolog | protein | 123 | 41% helix, 15% strand | B3S7S5 |
| C, D | DNA (5'- D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3') | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.48 | 0.73 | 20 | empty |
| 2 | 52 | 0.35 | 0.79 | 19 | empty |
| 3 | 105 | 0.34 | 0.74 | 14 | empty |
| 4 | 55 | 0.32 | 0.77 | 18 | empty |
| 5 | 51 | 0.26 | 0.73 | 11 | empty |
Interfaces
4 interfaces between chains.
- C–D · 856 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- A–C · 361 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 324 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 171 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5NM9 · Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site. · the same entry in another collection · chain A against A, TM-score 1.00
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 B3S7S5
- Elsewhere: RCSB PDB 5NM9 · PDBe 5NM9 · UniProt B3S7S5
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