Research workbench
Crystal structure of the MH1 domain of SMAD5-SMAD3 chimera construct bound to the ggcgc site
Analyse Crystal structure of the MH1 domain of SMAD5-SMAD3 chimera construct bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TBZ
- Type
- protein + DNA
- Length
- 159 residues
- Chains
- 3
- 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
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mothers against decapentaplegic homolog 5 | protein | 127 | 39% helix, 14% strand | Q99717 |
| B, C | 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 · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.68 | 0.76 | 63 | empty |
| 2 | 99 | 0.45 | 0.79 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 786 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- A–B · 363 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 211 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6TBZ · Crystal structure of the MH1 domain of Smad5-Smad3 chimera construct bound to the GGCGC… · 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 0.94
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 6TBZ · PDBe 6TBZ · UniProt Q99717
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