Research workbench
Crystal structure of the GGCT site-bound MH1 domain of Smad5 containing a GGGS insertion in the Loop1
Analyse Crystal structure of the GGCT site-bound MH1 domain of Smad5 containing a GGGS… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TCE
- Type
- protein + DNA
- Length
- 139 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.92
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Mothers against decapentaplegic homolog 5; DNA…
- UniProt
- Q99717
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · resolution 2.92 · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 5 | protein | 123 | 37% helix, 15% strand | Q99717 |
| B | DNA (5'-D(P*TP*GP*CP*AP*GP*GP*CP*TP*AP*GP*CP*CP*TP*GP*CP*A)-3') | dna | 16 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 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 | 62 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 377 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6TCE · Crystal structure of the ggct site-bound MH1 domain of SMAD5 containing a gggs insertion… · 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 A against A, TM-score 0.95
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 6TCE · PDBe 6TCE · UniProt Q99717
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.