MolNFT v1 · #149413 · protein + DNA
Crystal structure of SMAD5-MH1 bound to the ggcgc site.
6FZS · Mothers against decapentaplegic homolog 5: “Crystal structure of SMAD5-MH1 bound to the ggcgc site.”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #149413 on GenesisL1: 3D structure, binding sites…
- PDB
- 6FZS
- Type
- protein + DNA
- Length
- 284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog 5; DNA (5'…
- UniProt
- Q99717
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 5 | protein | 125 | 42% helix, 14% strand | Q99717 |
| B | Mothers against decapentaplegic homolog 5 | protein | 127 | 42% helix, 14% strand | Q99717 |
| C, D | DNA (5'- D(P*TP*GP*CP*AP*GP*GP*CP*GP*CP*GP*CP*CP*TP*GP*CP*A)-3') | dna | 16 | — | — |
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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.68 | 0.76 | 78 | empty |
| 2 | 204 | 0.46 | 0.74 | 27 | empty |
| 3 | 51 | 0.23 | 0.72 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 751 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- A–C · 347 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 333 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 185 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 180 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6FZS · Crystal structure of Smad5-MH1 bound to the GGCGC site. · the same entry in another collection · chain A against A, TM-score 1.00
- Q99717 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 5 (Q99717) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 Q99717
- Elsewhere: RCSB PDB 6FZS · PDBe 6FZS · UniProt Q99717
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