MolNFT v1 · #14679 · protein + DNA
Crystal structure of a smad MH1 domain bound to DNA
1MHD: “Crystal structure of a smad MH1 domain bound to DNA”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #14679 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1MHD
- Type
- protein + DNA
- Length
- 273 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA; SMAD3
- UniProt
- P84022
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA | dna | 13 | — | — |
| D | DNA | dna | 14 | — | — |
| A, B | SMAD3 | protein | 123 | 40% helix, 15% strand | P84022 |
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 | 758 | 0.68 | 0.76 | 64 | empty |
| 2 | 171 | 0.49 | 0.77 | 20 | empty |
| 3 | 108 | 0.40 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 597 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- C–A · 359 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–B · 337 Ų buried · 7 hydrogen bonds · protein-nucleic
- D–A · 234 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–B · 153 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1MHD · Crystal structure of a smad MH1 domain bound to DNA · the same entry in another collection · chain C against C, 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 0.96
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 1MHD · PDBe 1MHD · UniProt P84022
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