Research workbench
Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site
Analyse Crystal structure of the Smad3-Smad5 MH1 domain chimera bound to the GGCGC site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZMN
- Type
- protein + DNA
- Length
- 271 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.333
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Mothers against decapentaplegic homolog 3; DNA…
- UniProt
- P84022
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · resolution 2.333 · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 3 | protein | 120 | 45% helix, 15% strand | P84022 |
| B | Mothers against decapentaplegic homolog 3 | protein | 119 | 46% helix, 15% strand | P84022 |
| 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
- ACT · Acetate ion · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
- PGE · Triethylene glycol · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.58 | 0.77 | 37 | empty |
| 2 | 326 | 0.56 | 0.76 | 30 | empty |
| 3 | 136 | 0.43 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1234 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 763 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- B–C · 372 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–D · 214 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6ZMN · Crystal structure of the SMAD3-SMAD5 MH1 domain chimera bound to the ggcgc site · the same entry in another collection · chain A against A, TM-score 1.00
- P84022 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 3 (P84022) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P84022
- Elsewhere: RCSB PDB 6ZMN · PDBe 6ZMN · UniProt P84022
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.