Research workbench
Crystal structure of SMAD2 without exon -MH1 bound to the cagac site.
Analyse Crystal structure of SMAD2 without exon -MH1 bound to the cagac site. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H3R
- Type
- protein + DNA
- Length
- 278 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mothers against decapentaplegic homolog; DNA (5'…
- UniProt
- B7Z5N5
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mothers against decapentaplegic homolog | protein | 121 | 45% helix, 15% strand | B7Z5N5 |
| C, D | DNA (5'- D(P*GP*AP*GP*TP*GP*TP*CP*TP*GP*CP*AP*GP*AP*CP*AP*CP*TP*C)-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
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 | 231 | 0.53 | 0.77 | 33 | empty |
| 2 | 245 | 0.49 | 0.75 | 32 | empty |
| 3 | 115 | 0.38 | 0.75 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 812 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- A–C · 344 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–B · 281 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 254 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6H3R · Crystal structure of Smad2 without exon -MH1 bound to the CAGAC 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 B7Z5N5
- Elsewhere: RCSB PDB 6H3R · PDBe 6H3R · UniProt B7Z5N5
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